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601 - Exam 2 > 4.1 Regulation of Gene Expression > Flashcards

4.1 Regulation of Gene Expression Flashcards

1
Q

Gene expression is energetically

A

expensive

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2
Q

What are the 3 types of regulation at the DNA level? Do they all occur in prokaryotes and eukaryotes, or just one?

A
  • chromatin remodeling (in eukaryotes ONLY)
  • DNA rearrangement (both)
  • DNA amplification (both)
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3
Q

Overview of chromatin remodeling

A

DNA is tightly packed in heterochromatin and needs to be loosened for transcription
SO
chromatin remodeling is done by ATP-driven remodeling complex and histone modifications

  • only in eukaryotes
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4
Q

Describe ATP-driven remodeling complex

A
  • Nucleosome sliding
  • Using energy from ATP hydrolysis to rearrange
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5
Q

what is acetylated and methylated during histone modifications

A

Lys is acetylated
Lys or arg are methylated

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6
Q

Deacetylation of histones is done by

A

Histone deacetylases (HDACs)

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7
Q

What adds the acetyl group from acetyl-CoA during histone modifications?

A

Histone acetyltransferases (HAT)

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8
Q

Define epigenetics

A

Change in phenotype due to alterations in gene expression that aren’t caused by changes in nucleotide sequence but by covalent modifications in DNA or histone proteins

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9
Q

What change in gene expression (epigenetics) occurs in bacteria and eukaryotes?

A

Methylation of C in eukaryotes
Methylation of A in bacteria

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10
Q

Recombination can produce ___ via DNA splicing

A

antibodies

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11
Q

Describe DNA binding protein motifs

A

Positively charged motifs that can bind to negatively charged DNA
- A transcriptional regulator

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12
Q

Define operon

A

Multicistronic mRNA encoding information for multiple proteins
- In bacteria

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13
Q

Define regulon

A

Genes or operon under the same regulatory control
- Diff way of encoding genes
- In bacteria

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14
Q

What are the ways you can organize genes in bacteria?

A

Operon and regulon

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15
Q

What are the transcriptional regulators in bacteria?

A

Promoters
Activators
Repressors
Effectors

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16
Q

Define attenuation

A

Ensures proper transcription control via translation

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17
Q

Define antitermination

A

Preventing RNAP from termination

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18
Q

Define riboswitch

A

Regulation of gene expression via metabolite sensing RNA

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19
Q

Define promoters

A

Affinity for a sigma

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20
Q

Define activators

A

Bind to DNA and “activate” transcription by enhancing RNAP binding

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21
Q

Define repressors

A

Bind to DNA at the operator site and repress transcription

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22
Q

Define effectors

A

Molecules that bind to activators/repressors to activate or inactivate their activity

23
Q

What type of transcription regulation occurs in bacteria and eukaryotes? Define it.

A

Cascade regulation - regulator regulates another regulator to affect multiple downstream genes

24
Q

What 2 models are negative regulators of bacterial genes?

A

Inducer and corepressor model

25
Q

When is there transcription and no transcription in the inducer model

A
  • Involves the lac operon
  • Transcription = signal binds to repressor and prevents repressor from binding to operator
  • No transcription = repressor binds to operator in the absence of a signal
26
Q

When is there transcription and no transcription in the corepressor model

A
  • Involves trp operon
  • Transcription = repressor is w/o signal and can’t bind to operator
  • No transcription = repressor is bound to signal and binds to operator
27
Q

What does negative regulation mean?

A

When repressor is bound to operator there is NO TRANSCRIPTION

28
Q

What does positive regulation mean?

A

When signal binds to activator that binds to DNA there IS TRANSCRIPTION

29
Q

What is an example of positive regulation?

A

cAMP:CRP model

30
Q

Repressor abbreviation in lac operons

A

LacI

31
Q

In the lac operon, the repressor is induced by what signal

A

allolactose

32
Q

What happens when you have different levels of cAMP and glucose?

A

High cAMP = low glucose = transcription
low cAMP = high glucose =no transcription

33
Q

Describe what happens when you have high glucose and low cAMP

A

Allolactose is unable to bind to repressor
SO
Repressor binds to operator and there’s NO TRANSCRIPTION

34
Q

Describe what happens when you have low glucose and high cAMP

A

Allolactose binds to repressor and prevents it from binding to the operator
SO
TRANSCRIPTION

35
Q

Where does the CRP:cAMP complex bind?

A

Upstream of DNA promoter and bends DNA

36
Q

Describe attenuation in bacteria, what loops are formed

A

3:4 stem loop = transcription terminator b/c of poly U tail
2:3 stem loop = antiterminator
1:2 stem loop = transcription continues

37
Q

How many regions are there in mRNA that can form stem loop structures?

A

4

38
Q

Why does a ribosome terminate in bacteria transcription?

A

if there’s high trp and it forms 3:4 stem loop

39
Q

What are post-transcriptional regulations in bacteria?

A

RNA processing (cleavage of RNA and modification AND poly A tail)
RNA stability (endo and exonucleases AND translation of mRNA)

40
Q

What are the translational regulations during initiation in bacteria?

A

RBS
RNA structure
Translational coupling

41
Q

What are translation regulation during elongation in bacteria?

A

RNA structure
tRNA and AA availability

42
Q

Translational regulation is done by ___ RNA in bacteria. What does it do?

A

Antisense
- It can base pair in antiparallel fashion w/ DNA or RNA

43
Q

What are the post-translational regulators in bacteria?

A
  • Regulation of sigma^S via proteolysis
  • Protein folding
  • Allosteric regulation
44
Q

What is an example of a transcriptional elongation mechanism in bacteria?

A

Presence of pausing sites between genes in operons
- Ex: hairpin loop

45
Q

Define architectural proteins and give an example

A

They facilitate the interactions between distant sequences in the genome
- They allow the gene regulatory proteins to interact with transcriptional factors
- ex: HMG proteins

46
Q

T/F: eukaryotic TF can’t be both activators and repressors based on protein modification

A

False
They CAN

47
Q

Describe what happens during the regulation of gene expression by a steroid hormone cortisol

A

Steps:
1. GR is inactive due to binding with HSP
2. Cortisol binds to GR
3. GR is displaced from HSP
4. GR can now form dimer
5. Goes into nucleus and binds
6. Transcription can happen

48
Q

What are the post-transcriptional regulators in eukaryotes?

A

Alternative splicing, poly-A site choice, and RNA editing

49
Q

What are the translational regulators in eukaryotes?

A
  • Phosphorylation/dephosphorylation of eukaryotes
  • Translational repressors prevent initiation
  • RNA-mediated translational inhibition by miRNA
50
Q

What do translational repressors do?

A

They bind and disrupt interaction between 5’ cap and poly A tail and prevents the 43S complex from forming

51
Q

Describe the translational repression involving iron in eukaryotes

A

Translation: abundant iron inactivates IRE-BP and translation of ferritin mRNA occurs
No translation: no iron so IRE-BP bound to prevent translation

52
Q

Define ferritin

A

Iron storage protein

53
Q

Gene silencing by RNA interference is done by ___ in eukaryotes

A

miRNA

601 - Exam 2 (11 decks)

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