Lecture 22: Gene Regulation Flashcards
The basics?
Why do we need regulation for protein making?
Because protein making is expensive
ATP ain’t cheap, make sure you only make proteins tat you need
The basics
What are the 3 General types of genes?
- Constitutive
- Induced
- Repressed
The basics
Describe a constitutive gene
- Genes that are expressed continuously
- Always needed and always on
Ex. Actin promoters
The basics
Describe an induced gene
- Expressed in response to stimuli
- Transcribed upon some kind of of stimuli
Ex. Heat shock response
The basics
Describe a repressed gene
- Inhibited until they are needed
- For a specific cellular scenario only
Ex. DNA damage repair
The basics
What is a general transcription factor?
Binds to the promoter to increase RNA polymerase affinity
The basics
What is a specific transcription factor?
Binds to the regulatory sequences to control transcription
The basics
What is positive regulation?
Activator proteins bind to the activator and promote transcription
The basics
What is Negative regulation?
Repressor proteins bind to the operator and inhibit transcription
The basics
What are the two scenarios of positive regualtion?
- Default is on: produce mRNA. Switch off upon corresponding signal
- Default is off: molecular signal must combine with activator to bind and induce transcription
The basics
What are the two scenarios of negative regulation?
Same idea: os the repressor on until a signal arrives? Or is the repressor only “active” depending on a certain signal?
The basics
Where are promotors and control elements located in prokaryotes?
Promoters and control elements are proximal to the transcribed regions
The basics
Where are promotors and control elements located in eukaryotes?
Promoters and control elements are proximal but additional control elements are distal to the transcribed regions
The basics
How do proteins bind to DNA?
Protein domains bind to specific sequences of DNA
The basics
What do proteins actually see and interact with in major or minor groove?
Structural differences and hydrogen bonding contacts give each DNA sequence a unique code for proteins to bind to
Operons
What type of cells use Operons?
Prokaryotes
Operons
What is an operon?
a DNA seqeunce that contain regulatory sequences and multiple protein-coding seqeunces
Operons
How are Operons bundled?
In such a way that genes contribute to a similar cellular process
Operons
Operons are polycistronic, what does that mean?
Single mRNA produces multiple proteins
Lac Operon
What does the lac operon do?
Controls the production of proteins in response to lactose
Lac Operon
What energy source do cells prefer?
What does lactose act as?
Glucose, lactose acts as a back up
Lac Operon
What happens when a cell runs out of glucose?
They produce “stress signals” such as cAMP that causes changes in gene expression to adjust to the glucose shortage
Lac Operon
What is Beta Galactosidase?
What does it do?
- One of the products of the lac operon
- Catalyzes two main reactions
Lac Operon
What two reactions does Beta Glactosidase catalyze?
1) Hydrolysis of lactose into galactose and glucose
2) Isomeration of lactose into allolactose
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
Lac Operon
What does Lac Z code for?
Beta galactosidase
Lac Operon
What does Laz I code for?
Codes for Lac repressor, transcribed early such that unnecessary downstream transcription would be stopped
Lac Operon
What does Laz Y code for?
Codes for lactose permease, necessary for lactose to enter the cell
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
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
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
Lac Operon
Describe the Lac operon when
- Glucose is high
- Lactose is absent
- No activity
- Repressor is present
Lac Operon
Describe the Lac operon when
- Glucose is low
- Lactose is present
- High activity
- Repressor is present
Lac Operon
Describe the Lac operon when
- Glucose is low
- Lactose is absent
- No activity
- Repressor is present
Trp Operon
What does the Trp operon do?
- Genes necessary to make Trp
- Modulates mRNA production mid-transcription
Trp Operon
What inhibits the production of Trp?
Trp inhibits its own production
Trp Operon
What happens when trp binds to trp repressor?
No transcription
Trp Operon
What does the Trp repressor do?
- Binds to free tryptophan to repress operon expression (negative feedback)
- Similar system for most amino acids
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)
Trp Operon
What does abundant trp lead to?
- High tRNA
- Translation that occurs quickly, stem loop (3+4) terminates transcription
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
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
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
Prokaryotic Translational Control
What does an increase in protein demand catalyze?
- Increased ribosome synthesis
- Coordinated production of rRNA and rProteins
Prokaryotic Translational Control
What does one ribosomal protein on each operon act as?
A translational repressor
Prokaryotic Translational Control
What is a translational repressor?
- rProtein has higher affinity for rRNA
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)
Prokaryotic Translational Control
What happens when rProtein levels > rRNA ?
rProtein will not assemble with rRNA and instead bind to transcripts and act as repressors
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
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
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
- 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
RNA Based Translational Control Types
What do cisactivators do?
The mRNA you are translating regulates its own translation rate
- Example: aptamers and riboswitches
Recombination
What does recombination do?
Transposing the direction of a promoter to “switch different variants of a gene being transcribed”
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
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
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
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
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
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
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
Control elements of eukaryotic genes
How far away might distal elements be from the Open Reading frame?
- 1MB away
- Within Introns
- Other chromosomes
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)
