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BIOL2202 Genetics > Module 3--Regulation of gene expression > Flashcards

Module 3--Regulation of gene expression Flashcards

1
Q

What is promoter?

A

A length of DNA sequence “upstream” of the transcribed region

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2
Q

What is the function of promoter?

A

Regulates gene expression through interaction with proteins

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3
Q

Where is the RNA polymerase binding site in prokaryotes?

A

-35 & -10 regions of lac promoter (where sigma factor binds)

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4
Q

Where is the strand separation site?

A

-10 region (A=T rich sequence)

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5
Q

What is consensus sequence?

A

Ideal promoter sequence

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6
Q

What kind of promoter match the consensus sequence?

A

Strong promoter

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7
Q

Is lac promoter strong or weak under normal conditions?

A

Weak

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8
Q

What is the mechanism of the initiation of transcription?

A
  • Different sigma factors compete to bind to core polymerase
  • RNA polymerase slides along DNA
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9
Q

What conditions are required for lac operon promoter to be active?

A
  • Cell needs energy
  • Glucose not available
  • Lactose is available
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10
Q

What is stringent response?

A
  • Under good nutrition, sigma D binds to RNA polymerase (housekeeping genes–>growth)
  • Under poor nutrition, sigma S (stationary phase/starvation) binds to RNA polymerase

(housekeeping genes suppressed–>maintenance)

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11
Q

What is alarmone (ppGpp)?

A

An intracellular signal molecule that is produced due to harsh environmental factors

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12
Q

What is the function of alarmone (ppGpp)?

A

It binds to RNA polymerase which reduces affinitiy of RNA polymerase for sigma D, so sigma S and other stress sigmas can compete for binding

-This reduces transcription of housekeeping genes and increases transcription of stress (other) response genes

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13
Q

Alarmore (ppGpp) is produced by:

A

RelA or SpoT

(RelA+uncharged tRNA when amino acid starvation;

SpoT-glucose when glucose starvation)

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14
Q

Alarmone (ppGpp) is degraded by:

A

SpoT (SpoT+glucose when glucose abundance)

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15
Q

What are the other regulators of sigma factors?

A
  • Regulation of gene transcription
  • Regulation of mRNA stability
  • Inhibition of translation
  • Inactivation by proteolysis
  • Activation by removing inhibitory N-terminal amino acid extensions
  • Inhibition by high affinity binding of anti sigma factors
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16
Q

What is cyclic AMP (cAMP)?

A

A specific glucose starvation signal

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17
Q

What is the function of cyclic AMP (cAMP)?

A

It binds to CRP (cyclic AMP receptor protein) when glucose is not available

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18
Q

What is allolactose?

A

A modified form of lactose

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19
Q

What is the function of allolactose?

A

It binds to lac operon repressor when lactose is available, which prevents inhibition of lac operon transcription

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20
Q

What is signal transduction?

A

Complicated protein modification networks & small molecule signals

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21
Q

What is the function of transcription factors (TFs)?

A

Interact with promoters to facilitate RNA polymerase binding

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22
Q

What is the cellular response to environmental factors?

A

1) Receptors
2) Signal transduction (communicating/integrating)
3) Transcription factors (TFs) (responding)

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23
Q

What is the mechanism of regulation by peptide hormones?

A

1) Hormone binds to a receptor protein in the membrane of its target cell
2) Hormone/receptor complex activates cytoplasmic protein
3) Activated cytoplasmic protein transduces a signal to the nucleus
4) The signal induces a transcription factor to bind to DNA
5) The bound transcription factor stimulates transcription
6) The transcript is processed and transported to cytoplasm
7) mRNA is translated into proteins

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24
Q

What is the mechanism of regulation by steroid hormones?

A

1) Steroid hormone enters its target cell and combines with a receptor protein
2) Hormone/receptor complex binds to a hormone response element in the DNA
3) Bound complex stimulates transcription
4) Transcript is processed and transported to cytoplasm
5) mRNA is translated into proteins

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25
Q

What is the induction of genes by heat shock?

A

Under heat stress, heat-shock transcription factor (HSTF) is phosphorylated and induces transcription

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26
Q

What are the pathways of gene regulation in longevity in eukaryotes?

A
  • Good nutrition –> housekeeping genes –> growth/reproduction
  • Poor nutrition –> starvation signalling –> stress genes –> longevity/suppressed reproduction
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27
Q

What are the longevity inducers?

A
  • Dietary restriction
  • Decrease in insulin signalling (cellular glucose deficit)
  • AMP kinase (AMPK) signalling (energy depletion)
  • Amino acid signalling (amino acid deficit)
  • Decrease in mitochondrial function (energy depletion)
  • Decrease in temperature (decrease in metabolic rate)
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28
Q

What and where is the core promoter in Eukaryotes?

A

It is assembly site of preinitiation complex containing basal transcription factors and RNA polymerase II, and is immediately upstream of transcription start

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29
Q

What does core promoter in Eukaryotes contain?

A

It contains a TATA box, AT rich sequence (site of strand separation)

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30
Q

What and where is proximal element in Eukaryotes?

A

It is site of binding for activator proteins and is immediately upstream of promoter

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31
Q

How can proximal elements lose their activity?

A

Moves further upstream by more than a few tens of nucleotides

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32
Q

How to conduct molecular genetic analysis of gene regulation?

A

Gene regulatory sequence is ligated to the protein coding sequence of GUS reporter gene

-If promoter is active, GUS is expressed and cell turns blue

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33
Q

How to define the boundary of the core promoter?

A

Progessive 5’ deletion until GUS reporter gene is not expressed

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34
Q

What and where is enhancer/distal element in Eukaryotes?

A

It is a site of binding for special transcription factors and is at upstream of promoter and proximal control elements

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35
Q

How to define the boundary of upstream regulatory elements?

A

By linking upstream elements to core promoter

36
Q

How to enhance the activity of core promoter?

A

It is enhanced greatly by distal elements

37
Q

Transcription begins when polymerase is:

A

Phosphorylated

38
Q

What is the basal transcription factor assembly process?

A
  • TFIID (TATA binding protein) binds to TATA box & bends DNA sharply
  • Other basal factors assemble
  • RNA polymerase II holoenzyme binds to TFIID
39
Q

What is proximal element important for?

A

Important for constitutive expression of housekeeping genes

40
Q

What does high level gene transcription need?

A

Enhancers/Distal elements

41
Q

For non-housekeeping genes, why would transcription initiation be infrequent?

A

Gene has only promoter + proximal elements

42
Q

What is the function of enhancers/distal elements/response elements?

A

Precise control of gene regulation

43
Q

What is mediator complex and its function?

A

It bends DNA of regulatory region and brings distal elements to the promoter

44
Q

What is special transcription factors?

A

Nearly always positive regulators

45
Q

What is the structure of transcription factor?

A
  • DNA binding domain: recognizes 4-8 bp sequences
  • Dimerisation domain: most transcription factors are inactive as monomers
  • Activation domain: interacts with subunits of mediator or RNA polymerase II
46
Q

What happens if there are sequence changes in transcription factor genes?

A

Changes development and thus phenotype

47
Q

Why changes in transcription factor genes do not lead to complete disorder?

A

Transcription factors coordinate the activity of many genes that function together

48
Q

Why most natural gene variants do not change protein function, but only gene expression?

A

Changeing expression levels is easy, but changing protein function is difficult

49
Q

Does the position of enhancer has effects on its activity?

A

No, effects of enhancers are independent of position; they may be upstream, downstream or in an intron

50
Q

What is epigenetics?

A

Semi-heritable information encoded as molecular tags on the DNA and associated proteins (life experiences & developmental programs)

51
Q

What is the structure of nucleosome?

A

It consists of 8 histone proteins + ~200 bp of DNA

52
Q

What does access to DNA in vivo require?

A

Chromatin modification

53
Q

How can nucleosomes be compacted tightly together?

A

H1 is required

54
Q

What is the function of histone H3?

A

Regulates chromatin activity

55
Q

How is histone H3 modified?

A

Acetylation and methylation

56
Q

What is nucleosome in inactive state?

A

DNA condensed tightly and histones not easily be removed

57
Q

What is nucleosome in active state?

A

Histones can be removed

58
Q

How can histone be modified?

A
  • Reversible acetylation
  • Reversible methylation
  • Epigenetic tags added to histone
59
Q

What enzymes are used in reversible acetylation?

A
  • Histone acetyl transferase (HAT): adds acetyl group
  • Histone deacetylase (HDAC): removes acetyl group
60
Q

What enzymes are used in reversible methylation?

A
  • Histone methyl transferase (HMT): adds methyl group
  • Histone demethylase (HDM): removes methyl group
61
Q

Does H3K9 acetylation activate or inactivate gene?

A

Activate gene

62
Q

What does H3K4 methylation do?

A

Enhances active site

63
Q

Does H3K9 methylation activate or inactivate gene?

A

Inactivate gene

64
Q

What are epigenetic tags and what do they do?

A

Records of the developmental/envrionmental experience of an organism:

  • no change to nucleotide sequence
  • semi-heritable/dynamic process
  • can facilitate or inhibit normal transcriptional control
65
Q

What leads to DNA methylation?

A

H3K9 methylation

66
Q

What is DNA methylation?

A

DNA very tightly condensed = genes strongly off

67
Q

What are the examples of methylation of repetitve DNA?

A
  • Heterochromatin = centromeric and telomeric DNA (highly methylated and condensed)
  • Dispersed repeats: viruses and transposons dispersed throughout the genome (inactivated by methylation, become reactivated when host under stress)
68
Q

What is the effect of methylation in development?

A
  • Methylation from previous generation erased prior to embryo implantation
  • Remethylation coincides with developmental progression
69
Q

How can diet cause methylation?

A

Mother’s diet during development can influence the epigenetics of child

70
Q

What is DNA imprinting?

A

30-200 genes are differentially inactivated by methylation in gametes of males or females

71
Q

What is penetrance?

A

Probability of a gene to be expressed

72
Q

What affects penetrance?

A
  • Methylation of genes
  • Somatic methylation: environmental/developmental modification of penetrance
  • Imprinting: sex-specific modification of penetrance
73
Q

How is methylation of viruses & transposons?

A
  • Methylation of transposons is maintained in somatic cells, gametes and across generations
  • Demethylation: mobilization under severe stress
74
Q

What are the types of methylation?

A

1) Dynamic gene regulation: erased in early embryogenesis, re-established during lifetime
2) Imprinting: erased and re-established early in gamete formation
3) Suppression of transposons (by piRNA signalling): maintained indefinitely, but erased under stress
4) X chromosome inactivation: cell-by-cell decision in early female embryo

75
Q

What is X-chromosome compensation?

A

If males and females have different numbers of X chromosome:

-Gene expression must compensate for the difference in gene copy number

76
Q

What is transgene?

A

Gene integrated into the genome in a genetic engineering experiment

77
Q

What is co-suppression?

A

Normal gene and transgene are both suppressed, uses RNA interference as mediator of co-suppressioon

78
Q

How does transgene suppression work?

A
  • Suppressed transgene is methylated: transcription is inhibited
  • Transcripts are degraded
79
Q

What is RNA interference and how does it work in all Eukaryotes?

A

dsRNA processed into siRNA (=small interfering RNA), which directs proteins to degrade mRNA transcript and suppresses gene expression

80
Q

What is micro RNA (miRNA) and its function?

A

It is single-stranded RNA (ssRNA) and binds to 3’ end of mRNA transcript which blocks translation

81
Q

What is the mechanism similar to siRNA and miRNA?

A
  • RNA cut into small pieces
  • Combines with a RISC (RNA induced silencing complex)
  • RNA directs RISC to target nucleic acid, in which target identified by complementary base-pairing
82
Q

What is the pathway of RNA interference?

A

Dicer processes dsRNA into siRNA

1) Double stranded RNA cut into small fragments
2) Protein complex assembled with small RNA
3) RNA delivers RISC to complementary mRNA sequence

83
Q

What are the examples of silencing mechanisms?

A
  • mRNA degradation (siRNA)
  • Inhibition of translation (miRNA)
84
Q

Overview of small RNAs

A
  • RNA processing
  • Silencing complex assembly
  • Degradation
  • Translation inhibition
  • Chromatin remodeling
85
Q

What is parallel regulatory system?

A
  • RNA fragments produced in parallel with protein synthesis, which are byproducts of mRNA processing
  • Indicator of gene expression
86
Q

Summary of RNA function:

A
  • Defence against viruses
  • Suppressor of transposons
  • Regulator of development
  • Coordinator of chromatin remodeling
  • Systemic coordinator of gene expression

BIOL2202 Genetics (6 decks)

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