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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
PXR:RXR nuclear receptor in presence of ligand
- 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
26
glucocorticoid receptor
- example of enhancer driven transcription | - TF with a DNA binding domain, an activation domain, ligand-binding domain, and nuclear localization sequence
27
GR in absence of steroid
- GR present in the cytoplasm bound a heat shock protein
28
GR in presence of steroid (its ligand)
- 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
29
mediator
- 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
30
chromatin
- DNA packaged into nucleosomes
31
core particle
- octamer particle with two histones H3 H4 H2A and H2B proteins - DNA wrapped around core
32
histone tails
- have tails that are accessible for modification and transcriptional function
33
Histone H1
- linker histone residing on DNA between nucleosomes
34
histone modifications
- 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
HAT
- adds acetyl groups
36
HDAC
- removes acetyl groups
37
HMT
- adds methyl groups
38
KDM
- removes methyl groups
39
chromatin remodeling
- open and close chromatin to allow to deny access of transcription factors
40
chromatin remodeling carried out by
- histone modifications | - ATP-dependent complexes that move or restructure nucleosomes
41
nucleosome unwrapping
- can unwrap DNA from nucleosome to allow DNA binding protein access
42
nucleosome mobilization
- can move nucleosome around to allow for binding for transcription
43
nucleosome ejection
- Can get rid of nucleosome
44
histone dimer exchange
- can exchange one of the histones for another hone with different modification
45
DNA methylation and transcriptional control
- promoter (Cpg) is unmethylated and gene can be transcribed | - promoter (Cpg) is methylated and gene is silenced
46
what methylates the CpG promoters?
- DNA methyltransferase
47
methylation importance in imprinting and cancer
- tumor suppressor gene CpGs can be methylated and silence
48
common insulator binding protein
- CTCF
49
insulators and enhancers
- can block an enhancer from activating an adjacent gene
50
insulators and repressors
- can block the spread or activation of repressive chromatin from silencing the gene activity
51
chromosomal domains
- insulator-binding protein joins two insulators to form a loop and isolates sites of active or inactive transcription
52
barrier sequence
- prevents spread of heterochromatin to adjacent genes
53
alternative splicing
- exon skipping - intron retention - alternative 5' splice site - alternative 3' splice site - mutually exclusive exons
54
exon skipping
- splice 1 and 2 together, but skip over exon 3
55
intron retention
- keep one of the introns
56
alternative 5'/3' splice site
- start splice in different sites to form larger or smaller exon
57
mRNA editing
- some mRNAs change bases after transcription due to an editing mechanism - occurs in cytoplasm - only on specific mRNAs at defined sites; not widespread
58
transferrin
- blood protein that transports iron
59
transferrin receptor
- membrane protein that binds transferrin allowing iron to enter the cell - control at level of mRNA stability
60
iron is low - transferrin
- mRNA transferrin levels are high | - iron regulatory proteins bind transferrin receptor mRNA and stabilize it to protect it from degradation
61
iron is high - transferrin
- mRNA levels are low - iron regulatory proteins bind iron but do not bind iron regulatory elements. - transferrin receptor mRNA is degraded
62
ferritin
- iron binding protein that stores iron for future use - control at level of translation - iron response element at 5' end can block translation
63
cellular iron levels high - ferritin
- 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
cellular iron levels low - ferritin
- no need to store iron | - iron response element bind to iron regulatory protein and blocks translation
65
microRNA control of translation
- 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
Dicer
- further trims pre-miRNA followed by degradation of one strand by Argonaute and RISC
67
strong match with miRNA
- degrades mRNA
68
weak match with miRNA
- inhibits mRNA translation
69
P bodies
- processing bodies - cytoplasmic sites of translationally repressed RNAs and RNA degradation proteins - possible role in regulating RNA levels and translation
70
RNPs and storage droplets
- can form storage droplet by phase separation
71
regulation of translation by guanine exchange factors
- one response to stress condition is a reduction in protein synthesis - stress results in phosphorylation of translation initiation factors - reducing protein synthesis
72
regulation by GEF process
- 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
ubiquination result
- targets for degradation
74
SUMOylation result
- targets for degradation
75
phosphorylation result
- activity
76
acetylation result
- activity
77
methylation result
- activity
78
what happens to misfolded proteins?
- they are targeted for degradation by specific proteases | - phosphorylation allows degradation
79
how does degradation occur?
- occurs by the ubiquitin/proteasome system
80
ubiquitin/proteasome system?
- ubiquitin added to protein - forms proteasome - get two things - peptide fragments - later degraded further into amino acids - released ubiquitin
81
E1
- ubiquitin activating enzyme - adenylates ubiquitin and attaches it to a high energy thioester on the enzyme - recognized E2 enzymes
82
E2
- ubiquitin conjugating enzyme - receives activated ubiquitin from E1 - binds to specific E3 enzymes
83
E3
- ubiquitin ligase | - recognize specific proteins and transfers ubiquitin onto them
84
protein decay and the inflammatory response
- 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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