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BIOL 0280 UNIT 4 > Lecture 22: Gene Regulation > Flashcards

Lecture 22: Gene Regulation Flashcards

1
Q

The basics?

Why do we need regulation for protein making?

A

Because protein making is expensive

ATP ain’t cheap, make sure you only make proteins tat you need

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2
Q

The basics

What are the 3 General types of genes?

A
  • Constitutive
  • Induced
  • Repressed
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3
Q

The basics

Describe a constitutive gene

A
  • Genes that are expressed continuously
  • Always needed and always on

Ex. Actin promoters

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4
Q

The basics

Describe an induced gene

A
  • Expressed in response to stimuli
  • Transcribed upon some kind of of stimuli

Ex. Heat shock response

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5
Q

The basics

Describe a repressed gene

A
  • Inhibited until they are needed
  • For a specific cellular scenario only

Ex. DNA damage repair

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6
Q

The basics

What is a general transcription factor?

A

Binds to the promoter to increase RNA polymerase affinity

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7
Q

The basics

What is a specific transcription factor?

A

Binds to the regulatory sequences to control transcription

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8
Q

The basics

What is positive regulation?

A

Activator proteins bind to the activator and promote transcription

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9
Q

The basics

What is Negative regulation?

A

Repressor proteins bind to the operator and inhibit transcription

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10
Q

The basics

What are the two scenarios of positive regualtion?

A
  • Default is on: produce mRNA. Switch off upon corresponding signal
  • Default is off: molecular signal must combine with activator to bind and induce transcription
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11
Q

The basics

What are the two scenarios of negative regulation?

A

Same idea: os the repressor on until a signal arrives? Or is the repressor only “active” depending on a certain signal?

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12
Q

The basics

Where are promotors and control elements located in prokaryotes?

A

Promoters and control elements are proximal to the transcribed regions

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13
Q

The basics

Where are promotors and control elements located in eukaryotes?

A

Promoters and control elements are proximal but additional control elements are distal to the transcribed regions

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14
Q

The basics

How do proteins bind to DNA?

A

Protein domains bind to specific sequences of DNA

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15
Q

The basics

What do proteins actually see and interact with in major or minor groove?

A

Structural differences and hydrogen bonding contacts give each DNA sequence a unique code for proteins to bind to

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16
Q

Operons

What type of cells use Operons?

A

Prokaryotes

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17
Q

Operons

What is an operon?

A

a DNA seqeunce that contain regulatory sequences and multiple protein-coding seqeunces

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18
Q

Operons

How are Operons bundled?

A

In such a way that genes contribute to a similar cellular process

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19
Q

Operons

Operons are polycistronic, what does that mean?

A

Single mRNA produces multiple proteins

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20
Q

Lac Operon

What does the lac operon do?

A

Controls the production of proteins in response to lactose

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21
Q

Lac Operon

What energy source do cells prefer?
What does lactose act as?

A

Glucose, lactose acts as a back up

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22
Q

Lac Operon

What happens when a cell runs out of glucose?

A

They produce “stress signals” such as cAMP that causes changes in gene expression to adjust to the glucose shortage

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23
Q

Lac Operon

What is Beta Galactosidase?
What does it do?

A
  • One of the products of the lac operon
  • Catalyzes two main reactions
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24
Q

Lac Operon

What two reactions does Beta Glactosidase catalyze?

A

1) Hydrolysis of lactose into galactose and glucose
2) Isomeration of lactose into allolactose

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25
Q

Lac Operon

What does the lac operon contain?

A

Several major parts (genes), each with an operator and activator sequence

1) Lac Z
2) Laz I
3) Laz Y

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26
Q

Lac Operon

What does Lac Z code for?

A

Beta galactosidase

27
Q

Lac Operon

What does Laz I code for?

A

Codes for Lac repressor, transcribed early such that unnecessary downstream transcription would be stopped

28
Q

Lac Operon

What does Laz Y code for?

A

Codes for lactose permease, necessary for lactose to enter the cell

29
Q

Lac Operon

How is the lac operon negatively regulated?

A

1) Lac repressor binds tightest to O, but must bind to another O site to repress transcription

2) Allolactose binds to repressor, decreasing affinity for all operator binding sites

3) Allows for low level of gene expression

30
Q

Lac Operon

How is the lac operon positivley regulated?

A

1) cAMP binds to cAMP receptor protein (CRP), binding to cAMP allows this protein to act as TF and positivley regulate Lac operon -> high level of expression

2) Inhibitor must be removed first: BOTH lack of glucose and presence of lactose is necessary for high expression

31
Q

Lac Operon

Describe the Lac operon when
- Glucose is high
- Lactose is present

A

Low activity, repressor is removed but no activator because of lack of cAMP

32
Q

Lac Operon

Describe the Lac operon when
- Glucose is high
- Lactose is absent

A
  • No activity
  • Repressor is present
33
Q

Lac Operon

Describe the Lac operon when
- Glucose is low
- Lactose is present

A
  • High activity
  • Repressor is present
34
Q

Lac Operon

Describe the Lac operon when
- Glucose is low
- Lactose is absent

A
  • No activity
  • Repressor is present
35
Q

Trp Operon

What does the Trp operon do?

A
  • Genes necessary to make Trp
  • Modulates mRNA production mid-transcription
36
Q

Trp Operon

What inhibits the production of Trp?

A

Trp inhibits its own production

37
Q

Trp Operon

What happens when trp binds to trp repressor?

A

No transcription

38
Q

Trp Operon

What does the Trp repressor do?

A
  • Binds to free tryptophan to repress operon expression (negative feedback)
  • Similar system for most amino acids
39
Q

Trp Operon

What is the Trp Operon regulated by?
What does this regulation look like?

A

Regulated by negative feedback:
- Abundance of Trp binds and activates to repressor to stop gene expression

  • Generates attenuated RNA (causes premature termination of transcription)
40
Q

Trp Operon

What does abundant trp lead to?

A
  • High tRNA
  • Translation that occurs quickly, stem loop (3+4) terminates transcription
41
Q

Trp Operon

What does low trp lead to?

A
  • Leads to low tRNA
  • Translation stalls
  • Stem loop (2+3) forms in place of attenuator structure
  • Transcription completes
42
Q

Regulons

What are regulons?

A

They are a way though wich operons talk to each other

A group of functionally related operons controlled by a common regulator

43
Q

Regulons

What are examples of regulons?

A

CRP
- Activates transcription at other operons responsible for carbohydrate metabolism

Lex A
- repressor that inhibits expression of a regulon where all operons are responsible for DNA repair

44
Q

Prokaryotic Translational Control

What does an increase in protein demand catalyze?

A
  • Increased ribosome synthesis
  • Coordinated production of rRNA and rProteins
45
Q

Prokaryotic Translational Control

What does one ribosomal protein on each operon act as?

A

A translational repressor

46
Q

Prokaryotic Translational Control

What is a translational repressor?

A
  • rProtein has higher affinity for rRNA
47
Q

Prokaryotic Translational Control

When is translation repressed?

A
  • Translation is repressed until amount of rRNA and rProtein are matched (both are necessary for ribosome and translation)
48
Q

Prokaryotic Translational Control

What happens when rProtein levels > rRNA ?

A

rProtein will not assemble with rRNA and instead bind to transcripts and act as repressors

49
Q

Prokaryotic Translational Control

What happens when rRNA levels return to normal?

A

rProtein has higher affinity for rRNA they will dissociate from mRNA and form complete ribosomes, continuing translation

50
Q

Prokaryotic Translational Control

When does the stringent response occur?

A

It occurs during low levels of amino acids: tRNA is uncharged and ribosomes bind an uncharged tRNA, translation stalls

51
Q

Prokaryotic Translational Control

What occurs during the stringent response?

A

1) Uncharged tRNA in A site signals amino acid concentrations are low

2) ppGpp is produced by RelA (stringent factor) and acts as a second messenger

3) ppGpp binds to RNA polymerase altering promoter binding

52
Q
  • RNA Based Translational Control Types*

What do transcactivators do?

A
  • A different RNA molecule comes in and regulates the translation rate of your target mRNA
  • Examples: miRNA, rpoS
53
Q

RNA Based Translational Control Types

What do cisactivators do?

A

The mRNA you are translating regulates its own translation rate
- Example: aptamers and riboswitches

54
Q

Recombination

What does recombination do?

A

Transposing the direction of a promoter to “switch different variants of a gene being transcribed”

55
Q

Eukaryotic Gene Expression

What are the 7 levels that Eukaryotic cells are regulated by?

A

1) Remodel chromatin
2) Transcription
3) RNA processing
4) mRNA export
5) RNA silencing/degradation
6) Translational control
7) Posttranslational control/degradation

56
Q

Eukaryotic Gene Expression

What are key components of Chromatin Remodeling?

A

1) How tightly DNA is spooled around histones determines how easily they are transcribed

2) Covalent modifications on histone tails also play a big role

3) Histone modifications can also direct TF binding

57
Q

Chromatin remodeling

In regards to how tightly DNA is spooled around histones

Describe the difference between tightly wound and loosely wound histones

A

Tightly wound = heterochromatin, less expressed due to difficulty of access by polymerase

Loosely wound = euchromatin, more expressed bc easy to access by polymerase

58
Q

Chromatin remodeling

What is the chromatin remodeling complex?

What does it do?

A

The SWI/SNF is a chromatin remodeling complex that partially separates DNA from histones

59
Q

Chromatin remodeling

Describe the effects of covalent modifications on histone tails

What happens when lysine is on the tails?

What happens when lysine is acetylated?

A
  • Lysine (+) on the tails normally are attached to (-) DNA, locking the DNA on tightly and preventing transcription
  • Acetylation of lysine disrupts this electrostatic interaction, loosening the DNA and making transcription easier
60
Q

Chromatin remodeling

What is the point of Histone modifications?

A

1) Make DNA more/less accessible
2) Chemically label regions of DNA to direct transcription factor binding

61
Q

Control elements of eukaryotic genes

Describe distal vs. Proximal elements

A

Distal elements are found far away from the ORF

Proximal elements are directly 5’ adjacent to ORF

62
Q

Control elements of eukaryotic genes

How far away might distal elements be from the Open Reading frame?

A
  • 1MB away
  • Within Introns
  • Other chromosomes
63
Q

Translational controls

What are the 3 translational controls that Eukaryotic mRNAs are subjected to?

A

1) UnTranslated Region (UTR) - proteins bind to 3’ to inhibit translation

2) Initiation factors (IF) - are phosphorylated to inhibit translation

3) RNA interference (miRNAs)

BIOL 0280 UNIT 4 (6 decks)

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