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Genetics exam #3 > Gene regulation in EUK > Flashcards

Gene regulation in EUK Flashcards

0
Q

two types of transcription factors

  • ___________: required for binding RNA pol to core promoter
  • ____________: affect rate of gene transcription, 2-3% of humans encode regulatory factors
A

general

regulatory

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1
Q

transcription factors:

-proteins affecting _______ _________ (gene transcription)

A

RNA polymerase

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2
Q

regulatory transcription factors:

typically recognize ___-_____ DNA elements, which are control/regulatory elements

A

cis-acting

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3
Q

regulatory factors bind to regulatory elements
-___________: protein that enhances transcription
_____________: DNA seq. that activator binds
-__________: protein that inhibits transcription
__________: DNA seq. the repressor binds to

A

activator, enhancer

repressor, silencer

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4
Q

most eukaryotic genes are regulated by several factors:

  • ___________/___________ transcription initiation
  • factors modulated (_________ molecules, protein-protein ____________, and __________ mods)
A

stimulate/inhibit

effector molecules, protein-protein interactions, and covalent mods

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5
Q

alter composition of nucleosomes near promoter

A

combinational control

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6
Q

most eukaryotic genes are regulated by several factors:
-______________ can inhibit transcription
prevent binding of __________
recruit proteins that compact __________

A

methylation
activator
chromatin

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7
Q

structural features of regulatory transcription factors

-________: regions of protein with a function

A

domain

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8
Q

dominant feature of regulatory factors

why? bc it fits into major groove of DNA helix, recognized base sequences, and hydrogen bonding occurs

A

alpha helix

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9
Q

features such a Leucine Zipper Facilitate, the joining of two proteins

A

protein Dimerization (homo- and hetero-)

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10
Q

transcription factors that recognize regulatory elements:
-_____&______ regulation of transcription
-location of regulatory elements ________ ________
up to 100,000 bp upstream of core _________
can be downstream of core _______ in introns

A

up and down
highly variable
promotor
promotor

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11
Q

how do transcription factors affect RNA polymerase II?

  • interact with proteins that interact with ____ ____________
  • ________ & _________ (communicate effects of reg trans factors)
  • TFIID (general transcription factor, binds to _______ box, required to recruit RNA pol II to the ____________)
A
  • RNA polymerase II
  • TFIID and mediator
  • TATA, promotor
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12
Q

protein complex that mediates RNA pol II and reg transcription factors

A

mediator

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13
Q

_________ affect gene transcription

  • synthesized by ___________ ______
  • transported in ______ ________
  • cells take up _________
A

steroids
endocrine glands
blood stream
steroids

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14
Q

regulation transc factor that binds to steroids

A

steroid receptor

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15
Q

-
-

A
  • glucose sysnthesis
  • breakdown of protines
  • mobilization of fats
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16
Q

unlike steroids, most signaling molecules bind to receptors in the plasma membrane
-triggers ____________ signal

A

covalent modification with CREB protein

intracellular

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17
Q

covalent modification with CREB protein:

  • cAMP response element-binding protein (CREB)
  • reg transc factor
  • signaling by _________ in cAMP (cyclic adenosine monophosphate)
A

increasing

18
Q

chromatin remodeling:
-changing the structure of chromatin can affect ___________
closed conformation= more compaction, transcription difficult
open conformation

A

transcription

19
Q

chromatin remodeling:
Chromatin remodeling complexes
-all have _________ ________(ATP dependent chromatin remodeling)
-similar to DNA _____________(motor proteins that move along DNA)

A

ATPase subunit

translocases

20
Q

__________ variants modify structure of chromatin

-affect transcription

A

histone

21
Q
  • amino-terminal tail is variable, has different amino acids

- the charge of the tail can affect binding to proteins or DNA

A

histone code

22
Q

eukaryotic genes are flanked by ___________ free regions.

  • NFR~ 150bp
  • flanked by specific -1 & +1 ____________
A

nucleosome

nucleosomes

23
Q

activation of transcription requires modifications to _______________

A

nucleosomes

24
Q

many genes are flanked by nucleosome-free regions (NFR) and well-positioned nucleosomes.

A

silent

25
Q

activation of transcription:
activator proteins bind to enhancer seq. the enhancers may be close to the transcriptional start site or they be far away

A
  1. binding of activators
26
Q

activation of transcription:
activator proteins recruit chromatin remodeling complexes such as SWI/SNF, and histone modifying enzymes. nucleosomes may be moved, and histones may be evicted. some histones are subjected to covalent modification, such as acetylation.

A
  1. chromatin remodeling and histone modification
27
Q

activation of transcription:
general transcription factors and RNA polymerase II are able to bind to the core promotor and form a pre-initiation complex.

A
  1. formation of the pre initiation complex
28
Q

activation of transcription:
during _________, histones ahead of the open complex are covalently modified by acetylation and evicted or partially displaced. behind the open complex, histones are deacetylated and become tightly bound to the DNA.

A
  1. elongation
29
Q

__________ is rare in inverts, common in vetebrates.

-________% of mammalian DNA

A

methylation

2-7

30
Q

CpG islands near promotor

  • C & G connected by Phosphodiester linkage
  • 1000-2000bp
  • methylation inhibits transcription
A

transcriptional regulation via DNA methylation

-inhibits transcription

31
Q

methylation affects transcription in __ ways:

-methylation of CpG islands may ________ or _______ binding or reg transcription factors

A

2

enhance, suppress

32
Q

methylation affects transcription in 2 ways:

methyl-CpG-binding proteins bind to methylated CpG islands and recruit other _________ ________

A

inhibitor proteins

33
Q

methylation is inherited during ______ ________, de novo methylation

A

cell division

34
Q
  • functions as a boundary btween two genes
  • acts as barrier to chromatin changes
  • blocks effects of neighboring enhancers
A

insulators

35
Q

insulators may promote the formation of ________

A

loops

36
Q

5 methods of gene regulation

A 
control transcription
processing of pre-mRNA
RNA stability
RNA interference
control translation
37
Q

results in different polypeptide products from same gene

A

alternate splicing of pre-mRNA

38
Q

alternative splicing:

  • results in diff polypeptide products from _____ gene.
  • enables mRNA and ________ __________
  • prominence varies by ________ (yeast:
A

same
polypeptide variants
species

39
Q

regulate alt splicing

-what is the factor?

A

splicing factors

-modulate the spliceosome (repression-exon skipping)

40
Q

regulate alt splicing

-whats the factor?

A

splicing factors

-modulate the spliceosome (enhancement)

41
Q
  • minutes to months
  • stability can be regulated
  • poly A tails important to stability (avg 200 nucleosides long)
  • poly A binding protein enhancers stability (mRNA rapidly degrade after poly A tail ____________ to 10-30 nucleosides)
A

mRNA stability varies widely

decreases

42
Q

mRNA destabilizing agents:
_______________ ( )- located in 3’ untranslated region (3’-URT)
-proteins bind, enhancing _____________

A

AU rich Element (ARE)

degredation

43
Q

RNA interference:

  • ___________ (______): 21-23 nucleosides, partially complimentary to mRNA, silence translocation, encoded by 200 genes in humans
  • ______-___________ _____ (_______): 21-23 nucleosides, perfect match to mRNA, silence translation due to mRNA degredation
A

microRNAs (miRNAs)

short-interfering RNAs (siRNAs)

Genetics exam #3 (8 decks)

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