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BIOL2202 > Module 3: Genetic and Epigenetic Gene Regulation > Flashcards

Module 3: Genetic and Epigenetic Gene Regulation Flashcards

1
Q

Describe promotor-protein interactions

A

-35 region:
- RNA pol binding
- sigma factor binds here

-10 region:
- A-T rich sequence

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2
Q

Under what conditions is the Lac operon active?

A
  1. cell needs energy
  2. glucose not available
  3. lactose is available
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3
Q

Describe the stringent response

A

Under good nutrition:
- sigma D binds to RNApol
- 60-80% of genes transcribed, transcripts are very stable
- proteins involved in translation and other housekeeping functions

Under poor nutrition:
- Sigma S binds to RNApol
- housekeeping genes suppressed
- 10% of genes induced (stringent response genes)

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4
Q

Describe the function and properties of alarmone

A
  • aka ppGpp
  • binds to RNA polymerase
  • reduces affinity of RNApol for sigma D
  • sigma S and other stress sigmas can now compete for binding
  • produced by RelA and SpoT
  • RelA (amino acid starvation)
  • SpoT (glucose starvation)
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5
Q

What happens if glucose is not available (catabolite repression)

A
  • cAMP is a specific glucose starvation signal
  • cAMP binds to CRP
  • Lac -35 sequence does not match consencus
  • CRP and sigma S promotes strong binding of holoenzyme –> facilitates transcription
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6
Q

What happens if lactose is available?

A
  • allolactose signals lactose availability
  • allolactose binds to lac operon repressor –> prevents inhibition of lac operon transcription
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7
Q

Regulation by peptide hormones

A
  1. receptor protein is embedded in the membrane of the target cell
  2. peptide hormone binds to the receptor
  3. cytoplasmic protein signal is activated
  4. transcription factor in the cytoplasm is activated and imported into the nucleus
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8
Q

Regulation by steroid hormones

A

steroid hormones are hydrophobic
1. pass through the membrane
2. binds to cytoplasmic receptor
3. receptor and hormone enter nucleus and acts as a TF that regulates gene expression

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9
Q

Describe induction of heat shock genes

A
  1. heat stress causes phosphorylation of HSTF (pre-made, but inactive)
  2. HSTF binds to HSE and helps RNA pol II to initiate transcription of heat shock genes
  3. transcribes Hsp70 genes
  4. Hsp70 controls:
    - restoration of damaged proteins
    - stabilisation of membranes
    - changes to gene expression

induction of response genes in 30 seconds
suppression of housekeeping genes in 300 seconds

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10
Q

Longevity inducers

A

result in increased longevity, decreased growth and reproduction:
1. decreased temperature
2. decreased mitochondrial function
3. amino acid deficit
4. decreased insulin signalling (glucose deficit)
5. lack of food (dietary restriction)

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11
Q

Structure of core promotor

A
  • RNA pol II preinititiation complex assembly site
  • 30-100 bp upstream of transcription start
  • “TATA” box found in 25% of promotors
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12
Q

Proximal element structure and function

A
  • sites of binding for activator proteins
  • immediately upstream of promotor
  • lose activity if moved further upstream
  • increase promotor activity
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13
Q

Enhancer element function

A
  • site of binding for specific transcription factors
  • upstream of promotor and proximal control elements
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14
Q

Describe the experimental analysis of beta glucuronidase

A

GUS = beta glucuronidase
if GUS expressed, cell turns blue

  1. use a progressive 5’ deletion
    - this deletes successive upstream regulatory regions
    - if pollen grain continues to turn blue, core promotor is still in tact
    - when pollen grain is colourless, this is where the core promotor lies in the gene
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15
Q

Describe basal transcription factors in gene regulation (core promotor protein)

A

Assembly:
- TFIID binds to TATA box and bends DNA sharply
- other basal factors assemble
- RNA Pol II holoenzyne binds to TFIID –> bends the DNA
- initiates DNA strand separation –> promotes ‘melting in’ of RNA pol II

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16
Q

Proximal element binding proteins

A

Activator proteins:
- important for maximal expression of housekeeping or regulated genes

17
Q

Enhancer binding proteins

A
  • sites of binding for specific TFs
  • precise control of gene regultion
  • activity of enhancer is mediated through proteins that bind to it
18
Q

Transcription factor structure

A
  1. DNA binding domain (recognises DNA sequences)
  2. dimerisation domain
  3. activation domain (interacts with regulatory proteins)
19
Q

Promotor Bendin

A

Mediator complex:
- bends DNA of a regulatory region
- brings distal elements to the promotor

20
Q

H3K9 acetylation

A

gene active

21
Q

H3K9 methylation

A

gene inactive

22
Q

H3K4 methylation

A

enhances active state

23
Q

Methylation of repetitive DNA

A
  1. heterochromatin
    - centromeric and telomeric DNA highly methylated
    - highly condensed
  2. dispersed repeats
    - viruses and transposons
    - inactivated by methylation
    - become reactivated when host under stress
24
Q

DNA imprinting

A
  • occurs in gametes
  • genes imprinted in sperm are never imprinted in oocytes and visa versa
  • genes are differentially inactivated by methylation in gametes
  • imprinted genes observed as mutant phenotypes that depend on parent of origin
  • if gene is imprinted - dominance = none
25
Q

Four types of DNA methylation

A
  1. dynamic gene regulation
    - erased in early embryogenesis, re-established during lifetime
  2. imprinting
    - erased and re-established during early gamete formation
  3. suppression of transposons (by piRNA signalling)
    - maintained indefinitely
    - erased under stress
  4. X chromosome inactivation
    - one X chromosome is inactivated in each cell (in females)
26
Q

Describe co-suppression

A
  • When a normal gene and a transgene are both suppressed
  • suppression can spread to non-transgenic tissue –> RNA mediated
  • causes a loss of flower pigmentation
  • suppressed plant transgenes were methylated (transcription was inhibited) or transcripts were degraded
27
Q

siRNA

A
  • externally introduced dsRNA
  • directs proteins to degrade homologous mRNA
  • signal can spread to other cells
  • also mediator of co-suppression
28
Q

miRNA

A
  • natural cellular transcript
  • blocks tranlation
29
Q

piRNA

A
  • transcript degradation or chromosome remodelling
  • suppresses transposons in the germline
30
Q

Describe RISC

A
  1. a large dsRNA is diced into small double stranded interfering RNAs
  2. small interfering RNAs and proteins assemble into ribonucleoprotein particles
  3. small interfering RNA i a particle is unwound to produce an RNA-induced silencing complex
  4. RISC targets a sequence in a mRNA that is complementary to the interfering RNA
  5. RISC interfering RNA base pairs with its target in the mRNA
  6. if perfectly base-paired, the mRNA is cleaved and degraded
  7. if imperfectly base-paired, translation of mRNA is blocked

BIOL2202 (3 decks)

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