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

Lecture 22: Gene Regulation Flashcards

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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
*Lac Operon* What does the lac operon contain?
Several major parts (genes), each with an operator and activator sequence 1) Lac Z 2) Laz I 3) Laz Y
26
*Lac Operon* What does Lac Z code for?
Beta galactosidase
27
*Lac Operon* What does Laz I code for?
Codes for Lac repressor, transcribed early such that unnecessary downstream transcription would be stopped
28
*Lac Operon* What does Laz Y code for?
Codes for lactose permease, necessary for lactose to enter the cell
29
*Lac Operon* How is the lac operon negatively regulated?
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
*Lac Operon* How is the lac operon positivley regulated?
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
*Lac Operon* Describe the Lac operon when - Glucose is high - Lactose is present
Low activity, repressor is removed but no activator because of lack of cAMP
32
*Lac Operon* Describe the Lac operon when - Glucose is high - Lactose is absent
- No activity - Repressor is present
33
*Lac Operon* Describe the Lac operon when - Glucose is low - Lactose is present
- High activity - Repressor is present
34
*Lac Operon* Describe the Lac operon when - Glucose is low - Lactose is absent
- No activity - Repressor is present
35
*Trp Operon* What does the Trp operon do?
- Genes necessary to make Trp - Modulates mRNA production mid-transcription
36
*Trp Operon* What inhibits the production of Trp?
Trp inhibits its own production
37
*Trp Operon* What happens when trp binds to trp repressor?
No transcription
38
*Trp Operon* What does the Trp repressor do?
- Binds to free tryptophan to repress operon expression (negative feedback) - Similar system for most amino acids
39
*Trp Operon* What is the Trp Operon regulated by? What does this regulation look like?
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
*Trp Operon* What does abundant trp lead to?
- High tRNA - Translation that occurs quickly, stem loop (3+4) terminates transcription
41
*Trp Operon* What does low trp lead to?
- Leads to low tRNA - Translation stalls - Stem loop (2+3) forms in place of attenuator structure - Transcription completes
42
*Regulons* What are regulons?
They are a way though wich operons talk to each other A group of functionally related operons controlled by a common regulator
43
*Regulons* What are examples of regulons?
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
*Prokaryotic Translational Control* What does an increase in protein demand catalyze?
- Increased ribosome synthesis - Coordinated production of rRNA and rProteins
45
*Prokaryotic Translational Control* What does one ribosomal protein on each operon act as?
A translational repressor
46
*Prokaryotic Translational Control* What is a translational repressor?
- rProtein has higher affinity for rRNA
47
*Prokaryotic Translational Control* When is translation repressed?
- Translation is repressed until amount of rRNA and rProtein are matched (both are necessary for ribosome and translation)
48
*Prokaryotic Translational Control* What happens when rProtein levels > rRNA ?
rProtein will not assemble with rRNA and instead bind to transcripts and act as repressors
49
*Prokaryotic Translational Control* What happens when rRNA levels return to normal?
rProtein has higher affinity for rRNA they will dissociate from mRNA and form complete ribosomes, continuing translation
50
*Prokaryotic Translational Control* When does the stringent response occur?
It occurs during low levels of amino acids: tRNA is uncharged and ribosomes bind an uncharged tRNA, translation stalls
51
*Prokaryotic Translational Control* What occurs during the stringent response?
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
* RNA Based Translational Control Types* What do transcactivators do?
- A different RNA molecule comes in and regulates the translation rate of your target mRNA - Examples: miRNA, rpoS
53
*RNA Based Translational Control Types* What do cisactivators do?
The mRNA you are translating regulates its own translation rate - Example: aptamers and riboswitches
54
*Recombination* What does recombination do?
Transposing the direction of a promoter to "switch different variants of a gene being transcribed"
55
*Eukaryotic Gene Expression* What are the 7 levels that Eukaryotic cells are regulated by?
1) Remodel chromatin 2) Transcription 3) RNA processing 4) mRNA export 5) RNA silencing/degradation 6) Translational control 7) Posttranslational control/degradation
56
*Eukaryotic Gene Expression* What are key components of Chromatin Remodeling?
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
*Chromatin remodeling* In regards to how tightly DNA is spooled around histones Describe the difference between tightly wound and loosely wound histones
Tightly wound = heterochromatin, less expressed due to difficulty of access by polymerase Loosely wound = euchromatin, more expressed bc easy to access by polymerase
58
*Chromatin remodeling* What is the chromatin remodeling complex? What does it do?
The SWI/SNF is a chromatin remodeling complex that partially separates DNA from histones
59
*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?
- 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
*Chromatin remodeling* What is the point of Histone modifications?
1) Make DNA more/less accessible 2) Chemically label regions of DNA to direct transcription factor binding
61
*Control elements of eukaryotic genes* Describe distal vs. Proximal elements
Distal elements are found far away from the ORF Proximal elements are directly 5' adjacent to ORF
62
*Control elements of eukaryotic genes* How far away might distal elements be from the Open Reading frame?
- 1MB away - Within Introns - Other chromosomes
63
*Translational controls* What are the 3 translational controls that Eukaryotic mRNAs are subjected to?
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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