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medical science xy1110 > genetics 8 > Flashcards

genetics 8 Flashcards

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USMLE® Step 1 flashcards Biology 101 flashcards
1
Q

what are eukaryotic genes regulated by

A
  • promotors - core and proximal
  • up/down stream - silencers and enhancers
  • introns and exons - splicing of introns
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2
Q

what do distal/proximal enhancers do

A
  • bind to transcription factors
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3
Q

what do core promotors do

A
  • general transcription factors - TATA box - RNA polymerase
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4
Q

what does the promotor compartmentalisation do

A
  • CCCTC binding factor
  • zinc-finger DNA binding protein
  • form DNA loops with cohesion
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5
Q

what is the function of promotor compartmentalisation

A
  • Enhancer-promoter interactions
  • Insulation against non-specific regulatory signals
  • Transcriptional activator
  • Stable chromatin loops - differentiation
  • CTCF loop formation/loss
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6
Q

what are the functions of transcriptional activators

A
  • promotes binding of other regulators
  • release DNA polymerase to start
  • recruits DNA polymerase
  • release DNA polymerase from pause
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7
Q

what are the functions of transcriptional repressors

A
  • Competitive DNA binding
  • Masking activation
  • Interact with Transcription actors
  • Recruit chromatin remodelling complexes
  • Recruit histone deacetylases
  • Recruit histone methyl transferase
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8
Q

what happens with positive effector mediated regulation

A
  • transcription factor binds
  • RNA polymerase recruitment
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9
Q

what happens with negative effector mediated regulation

A
  • repressor protein binds
  • prevents gene expression by blocking RNA pol binding or block RNA pol movement
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10
Q

what are operons

A
  • group of related genes under the same promotor
  • inducible or repressible
  • many in bacteria
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11
Q

when is Iac operon in E.coli lactose metabolism turned off and on

A

off - presence of glucose
on - presence of galactose or inducer (PTG)

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12
Q

how is Iac operon turned off in the presence of glucose

A
  • repressor (homo tetramer) binds to operator
  • reduce RNA polymerase activity
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13
Q

how is Iac operon turned on

A
  • lactose metabolite (allolactose) inhibits Iac I repressor
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14
Q

what happens to Iac enhancer when there is no/low glucose

A
  • low ATP –> cAMP increases —-> metabolism of other sugars
  • CAP-cAMP binds to promotor
  • enhancer RNA polymerase binds
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15
Q

what does trp operon do

A
  • five enzymes necessary for tryptophan biosynthesis
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16
Q

how is trp operon transcriptionally controlled

A
  • repressor binds to operator
  • loop termination of mRNA synthesis via leader gene
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17
Q

what happens when the histones are acetylated or ubiquitinated

A
  • N-terminal (lys)
  • reduces + ve charge
  • disrupts DNA binding
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18
Q

when a chromatin is decondensed what happens

A
  • actively transcribed
  • accesible to transcription factors
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19
Q

what occurs in RNA polymerase II transcription

A
  • Histones ahead ubiquitinated
  • Removed by histone chaperones
  • Inserted behind
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20
Q

what does the chromatin remodelling factor do

A
  • alters nucleosome structure
21
Q

what are high mobility group proteins (HMGP)

A
  • associated with active chromatin
  • modify DNA histone interaction
  • recruit transcriptional activators
22
Q

what does DNA methylation act on

A
  • DNA methyl transferase
  • cytosine
23
Q

what can deletion mapping do

A
  • delete genetic regions
  • increase/decrease expression
  • change phenotype
  • identify function
24
Q

how does DNase hypersensitivity assays work

A
  • cut DNA
  • fragments cloned/ sequenced
  • identify areas of DNA loosely attached to histones
  • active areas
25
Q

what does DNase I do in hypersensitivity assay

A
  • cuts ssDNA or dsDNA
  • digests easy accessible regions
26
Q

what does Mg2+ do in the hypersensitivity assays

A
  • randomly cuts dsDNA strand independently
27
Q

what does manganese (Mn2+) do in the hypersensitivity assays

A
  • cleavers both DNA strands
  • same site
  • blunt ends or 1-2 nucleotide overhang
28
Q

what does DNase hypersensitivity assays show us

A
  • differences in active areas eg. cell type, tissues, conditions
29
Q

what does recombinant receptor assays do

A
  • fusion of promotor to reporter gene
30
Q

what does recombinant reporter assays tell us

A
  • expression levels
  • time during cell cycle
  • induction / repression
31
Q

what are the common assays in recombinant reporter assays

A

Green fluorescent protein (GFP)
Luciferase assay - luciferase/luciferin
GUS assay - β-glucuronidase/X-Gluc, PNG or MUG
Blue-white screen - β-galactosidase/X-gal

32
Q

what are the components of gene regulation

A
  • transcription factors
  • genera transcription factors
  • RNA polymerase
  • chromatin remodelling complexes
  • histone modifying enzymes
33
Q

what is regulatory proteins function

A
  • activate or deactivate different genes so:
  • respond to environment - food intake, temperature
  • cell growth and division
  • development - embryonic and muscle cells
  • polarisation/ iocomotion
  • cell-cell communication
34
Q

what are the corticosteroids mode of action

A
  • Bind glucocorticoid receptors (GR)
  • Bind glucocorticoid response elements (GRE)
  • Histone H4 acetylation
  • Anti-inflammatory genes
35
Q

what happens when there is a high does of corticosteroids

A
  • anti-inflammatory gene expression
36
Q

what does oestrogen receptor antagonists do

A
  • prevent/delay reccurence of breast tissues
37
Q

what does tamoxifen do

A
  • competitively binds to oestrogen receptors
38
Q

what is an example of a helix-turn-helix motif

A
  • tryptophan repressor
  • binds as dimer at palindromic site
  • type 2 restriction enzymes cut sites are palindromic
39
Q

what do cys-cys-his-his family do

A
  • zinc finger motifs
  • zinc holds alpha helix and beta pleated sheets together
  • chains of zinc fingers
40
Q

what do leucine zipper motifs do

A
  • y shaped structure
  • DNA binding and protein dimerisation
  • leucines hold helices together
  • DNA binding in major grove
41
Q

what do DNA loop helix do

A
  • two alpha helices connected by a loop
  • short- dimerisation and long - interacts with DNA
  • regulated by interacting partner
42
Q

what is an example of a loop region

A
  • p53
  • tumour supressor protein
  • major and minor groove
43
Q

what do coactivators and corepressors do

A
  • don’t bind directly to DNA
  • bind to DNA binding proteins (premiscous)
  • scaffolds for other proteins
44
Q

what do intergenic regions do

A
  • prevent harmful transcription
45
Q

what happens when a cell is methylated

A
  • high dividing cells —> higher expression
  • low dividing cells –> lower expression
46
Q

what occurs with CpG islands

A

-1000bp
- often not methylated
- fewer associated nucleosomes
- methylation —> gene silencing

47
Q

what do iron response elements do

A
  • binds to iron response element binding protein
  • regulate iron metabolism
48
Q

what does ferritin do

A
  • helps to store iron
  • IRE at 5’ of mRNA
  • low iron –> IRP binds IRE –. prevents translation
  • high iron –> IRP binds iron –> translation increases –> iron storage
49
Q

what does transferrin- receptor do

A
  • iron uptake
  • IRE at 3’ on mRNA
  • low iron —> IRP binds to IRE –> mRNA stable –> increase iron uptake
  • high iron –> IRP binds iron –> mRNA degraded

medical science xy1110 (40 decks)

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