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BIO 226 > 8 (9) Regulation of Gene Expression in prokaryotes > Flashcards

8 (9) Regulation of Gene Expression in prokaryotes Flashcards

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1
Q

what are the layers of control

A
  • Transcriptional
    ○ How much rna is made
  • mRNA processing
    ○ How quickly RNA is degraded
  • Translation
    ○ How much protein is made
  • Protein function
    ○ stability
    § How quickly protein is degraded
    ○ Regulation
    § Where will proetin localize
    § What others will it interact with
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2
Q

what is controlled transcription

A
  • Both intra and intercellular communication is important in this regulation
    • Affeccted by environmental factores
      ○ Heat, light, signalling molecs
    • +ve and -ve regulatory proteins called transcription factors (TFs)
      ○ Bind to specific regions of DNA
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3
Q

what is a response element

A

binds to a TF

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4
Q

what is signal transduction

A

going from the environment to a gene

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5
Q

what is transcriptional regulation in proks

A

○ RNA polymerase can bind all the promoters
- Function increased by activators and decreased by repressors

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6
Q

what is transcriptional regulation in euks

A

○ RNA polymerase cant bind promoter on its own
○ Several levels of protein interaction required
§ Uses TATA box
○ Euks much more complicated than proks

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7
Q

what are the gene regulatory elements

A

Enhancers
special TFs
General TFs
coactivators

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8
Q

what do enhancers do

A

○ Regions of DNA that bind TFs
○ Tissue and condition specific
○ Can be proximal or dital (close or far)
○ Can be found all over the place

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9
Q

what do special TFs do

A

○ Specific to a subset of genes
○ Binds to enhancers
§ Use that to bind RNA polymerase or other TFs
○ Bind proximal enhancers

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10
Q

what do general TFs do

A

○ Generic
○ Bind all promoter regions
○ Promotes RNA polymerase binding

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11
Q

what do coactivators do

A

○ Bind TFs to promote transcription
○ Like inducers but are proteins

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12
Q

what are the regulatory elements that prevent transcription

A

Silencers(cis)
Repressors(trans)
corepressors

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13
Q

how do silencers regulate/prevent transcription

A
  • DNA regions for transcription factor binding
  • often tissue/situation specific
  • same function as the operator
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14
Q

how do repressors regulate/prevent transcription

A
  • transcription factors
  • bind to silencers
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15
Q

how do corepressors regulate/prevent transcription

A
  • bind TFs to promote transcription
  • like prok corepressors but can be proteins
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16
Q

what are the domains found in transcription factors

A
  • always have transcription binding domain
  • protein-protein interactions domains
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17
Q

what are the protein interaction domains

A
  • dimerization
  • activation and repression domains
  • ligand binding domains
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18
Q

What is the enhanceosome

A
  • recruits chromatin modifiers
  • grp of proteins and TFs that assemble on specific DNA region - enhancer.
  • structure helps activate gene transcription
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19
Q

what do insulators do

A

tangles the DNA strand so that enhancers are unable to activate genes close to them

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20
Q

what is the Gal pathway

A

the euk version of the LacOperon

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21
Q

what happens if galactose is present

A

○ Expression of genes req to break galactose –> glucose are increased 1000x
○ Going from sugar to better sugar

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22
Q

what is the Gal4

A

○ TF that binds to the enhancers of all the genes
○ When activated transcription for all the genes will proceed
○ Binds DNA (enhancer)
○ Brings activation domain to the promoter
○ Helps recruit RNA polymerase

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23
Q

what regulates Gal4

A

Gal80 and galactose

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24
Q

TF Gal4 in the Gal Pathway is = the activator of the LacO path

A

T

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25
Q

what is chromatin

A

packages DNA
- DNA + Histones

26
Q

____ base pairs are wrapped ___ around a histone octamer

A

146
7x

27
Q

how many copies of histones are there in each histone core

A

2

28
Q

TF Regions with lots of chromatin are hard to transcribe

A

T

29
Q

what are some traits of closed chromatin (heterochromatin)

A

○ Dense dark regions
○ Often associated with histone methylation
○ High density region
○ Nothing happening to them pretty much

30
Q

what are traits of open chromatin (euchromatin)

A

○ Low density region
○ Associated with acetylation of histone
○ Things happen here

31
Q

TF Spreading heterochromatin cannnot silence genes

A

F, it can

32
Q

how does heterochromatin silence genes

A
  • Affects expression of nearby genes
  • Can cause “position effect variegation”
  • Can turn gene on or off based on where the heterochromatin is located
33
Q

Nucleosomes are specifically position along genes to influence _________

A

Transcrition

34
Q

what can be said about the placement of chromatin along the DNA strand

A
  • enhancers are wrapped nucleosome repressed genes
  • the promoter is often free of nucleosomes
35
Q

what is chromatin remodelling

A
  • Process of moving histones out of the way
  • Can be post-tranlationally modified by adding a methyl, acetyl, or phosphate grp
36
Q

TF in chromatin remodelling Each tail can be modified at different positions

A

T

37
Q

what is the histone code

A

-modifying histone tails

38
Q

what does the histone code use to regularly modify histone tails

A

Chromatin reader: follows instructions
Chromatin writer: adds modification
Chromatin eraser: removes modification
Chromatin remodeller: moves histones

39
Q

what are the different modifications the histone code makes

A

○ Methylation
§ Reduce probability transcription
○ Acetylation
§ Increase probability transcription
○ Phosphorylation

40
Q

what is the

A

Order of steps to activate transcription in euks
- Cell detects virus
- Enhansosome forms from enhancer
- Chromatin writers are recruited by enhansosome
- Chromatin readers loosen promoter nucleosome
- Initiation complex forms
- RNA polymerase binds and transcription starts
- Eraser proteins remove chromatin mods
- TFs and readers release
- Chromatin resilences the gene

41
Q

what are 3 facts about heterochromatin

A
  • Grows and shrinks
  • Prevents transcription
  • Can be modified via chromatin remodellers
42
Q

TF DNA methylation regulates transcription

A

T

43
Q

how does DNA methylation regulate transcription

A

○ Usually added to a C next to a G (CpG)
○ Affects gene and chromatin regulation

44
Q

what is a CpG island

A

○ 200-4000 CpGs together
○ Mostly on gene promoters
○ Calls for heterochromatin

45
Q

TF DNA methylation can be bad for you

A

T

46
Q

how can DNA methylation be bad for you

A
  • Can indicate tissue type
    ○ Turns off brain proteins in ur muscles
  • Plays a role in disease
    ○ Can look at the methylation patter in cells and can detect a virus
47
Q

How do modifiers alter gene regulation

A
  • Histone and DNA mods repress and activate transcription
  • Reader proteins (mCpG + CpG) bind to regulatory sequences DNA and histone modification
  • Chromatin modifiers (writers+erasers+remoedllers) recruited by reader proteins
  • Histones and DNA are modified accordingly
  • TF complexes assemble affecting RNA polymerse recruitment (is activated)
48
Q

what are the functions of Epigenetics

A
  • maintain cell differentiation
  • maintain hetero/euchromatin
  • dosage compensation
  • X-chromosome inactivation
49
Q

what are the 2 layers of control in epigenetics

A
  • Cytoplasmic control of mRNA stability
  • RNA interference (RNAi)
50
Q

how does cytoplasmic control of mRNA stability work

A

○ Influenced by several factors
○ Poly A tail
○ 3’ UTR sequence
○ Chemical factors
○ Small interfering RNAs (siRNA) or microRNAs (miRNA)

51
Q

what is RNAi (RNA interference)

A

Short non coding RNAs regulate gene expression
○ Small interfering RNAs (siRNA)
- microRNAs (miRNA)

52
Q

how does RNAi work

A

○ Binds to RNAs to create dbl stranded RNA
§ Cell thinks its virus
§ Breaks the RNA

53
Q

what is the specific job of RNAi

A

reduce expression of target gene by removing mRNAs to prevent transcription

54
Q

what are the dsRNA sources

A

§ Exogenous dsRNAs
§ Endogenous dsRNAs
§ Dicer

55
Q

what are Exogenous dsRNAs

A

□ Long dsRNAs from foreign sources like transgenes and viral genes

56
Q

what are endogenous genes

A

□ microRNA genes
□ Small non-coding RNA that forms a hairpin

57
Q

what is a dicer

A

□ Chops dsRNA up into bits
□ Bits called siRNA (small interfering RNA) if theyre from longer dsRNAs (exogenous)
□ Called MicroRNAs (miRNAs) if they come from endogenous dsRNAs (shorter)

58
Q

what does RICS do

A

§ Binds to a small bit of dicer product (si or mi RNAs)
§ Splits the strands
§ Takes complimentary strand as a guide to get more and chop those up

59
Q

what is an RNAi phenocopy

A
  • Wild type that looks just like the mutant
60
Q
A

BIO 226 (10 decks)

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