Gene Regulation Flashcards
What level of central dogma are most genes regulated?
Transcription level
What’s a somatic cell?
Non-sex cells
How do we know that all cell types share the same genome? (frog)
Destroy unfertilized egg nucleus with UV light; inject nucleus from frog skin cells; normal tadpole grows
What steps can eukaryotic gene expression be controlled at?
- transcriptional
- RNA processing control
- RNA transport, localization control
- Translational control
- mRNA degradation control
- Protein activity control
Tyrosine aminotransferase gene - what’s the point of the example with it?
It only appears in the liver, so there’s tissue-specific expression
Why don’t you need to open DNA double helix to know what base pairs there are?
You can look at edges of major/minor groove and know nucleotide
Where do most gene regulatory proteins bind?
Major groove of DNA
What kinds of structural motifs are on gene regulatory proteins?
Homeodomain proteins, leucine zippers, helix-turn-helix, etc
Around how many nucleotides are the binding sequences of most proteins?
Roughly 8, giving about 200,000 binding sites in the human genome assuming it’s random.
What is the relationship between operators and operons? What species can you find them?
Operators are in the promoter. When no repressors are bound to them, they’re turned on. They are in prokaryotes.
Where does the tryp repressor bind? What does it do?
They bind to operators.
They prevent polymerase from binding.
What does the tryp repressor need to itself become active?
Tryptophan binding to it
What happens when tryptophan is low?
It won’t bind to the repressor, so the repressor will be inactive and its operon will be on
What happens when tryptophan is high in regards to operons?
Tryptophan binds to the tryp repressor, and then the tryp repressor binds to operator, preventing tryptophan transcription
How can transcription be enhanced?
Activator proteins can bind, which pull RNA polymerase in
What are cis-regulatory sequences?
Any sequence of DNA that controls gene expression. Example in class showed one far away from promoter.
How many transcription regulators is the lac operon controlled by?
Two
What does the lac operon need to be on?
-glucose, +lactose.
CAP is bound, repressor is off
What does -glucose do in terms of the lac operon?
CAP protein (activator protein) gets cAMP and binds to regulatory sequence to pull polymerase in
What does -lactose do in terms of the lac operon?
The Lac repressor gets activated, binds to a regulatory sequence, and prevents polymerase from going.
What is the Lac operon useful for? Is it in prokaryotes or eukaryotes?
To digest lactose when there isn’t enough glucose present. Prokaryotes.
What’s a repressor and what does it do? To what regulatory sequences can it bind?
It’s a protein that binds to DNA. Stops polymerase from binding or slows down transcription somehow. Binds to silencers or operators.
What does ADEPT stand for?
Analogy, Diagram, Example, Plain-english, Technical
What are cis regulatory sequences bound by?
Gene regulatory proteins / transcription factors
Why are cis regulatory sequences cis?
They are on the same chromosome as the gene to be transcribed
What binds to CAP in regards to the LAC operon? What happens when CAP is bound? When is it bound?
Cyclic-AMP. Turns on expression of LAC operon. Binds when there’s no glucose present.
What is a plasmid in relation to prokaryotes?
Little circles of DNA separate from the normal circular chromosomal DNA. Independently replicated.
What is the difference between enhancers and promoters?
Enhancers are bound by activators and increase likelihood of transcription
Promoters are located near start sites and bind RNA polymerase.
(Mostly eukaryotes) How can a protein hundred of nucleotides away cause a change in gene activation? What protein complex is involved here?
DNA can loop around. Regulatory proteins can bind to areas on the mediator protein complex, which has a ton of surface area for potential binding
What is the difference between enhancers and operators?
Enhancers increase rate of transcription when activator proteins bind. They are in both eukaryotes and prokaryotes. They are far away from the promoter.
Operators stop transcription completely when repressors bind. They are only in eukaryotes and control operons. They physically block polymerase at promoters.
What is the difference between promoters and operators?
Promoters are located near start sites (TATA) and bind RNA polymerase
Operators stop transcription completely when repressors bind. They are only in eukaryotes and control operons. They physically block polymerase at promoters.
Are gene regulatory proteins always by themselves?
No, they assemble into complexes all the time.
What’s the difference between in vivo/in vitro in regards to gene regulatory sequences?
In vivo activators associate with each other all the time, they’re separate in vitro
What’s a coactivator protein? Can RNA bind to them?
Binds to proteins already bound to DNA instead of to DNA directly. RNA can bind to them as well.
What do co-repressor proteins do?
Bind to proteins already bound to DNA to turn off genes
If a transcription regulator binds to nucleosomes, what new protein could that recruit?
The chromatin remodeling complex, to change structure
What kinds of changes can the chromatin remodeling complex cause?
Sliding (increase DNA access)
Nucleosome removal (let transcription machinery in)
Histone replacement (variants let DNA get accessed easier)
Change pattern of modification
What enzyme might be involved in changing patterns of chromatin modification?
Histone-modifying enzyme
Histone acetyl transferase - what on histones does it affect? What does it recruit?
The tails. It’s a coactivator, comes in, recruits kinase, and phosphorylates a serine
If you have a phosphorylated histone caused by histone kinase/acetyl transferase, what does it recruit?
Chromatin remodeling complex;
For chromatin remodeling, does one protein generally cause changes in transcription?
No; there’s normally a cascade, and multiple kinases, transferases, etc are recruited to eventually cause transcriptional changes
What do activator proteinst do to make more DNA get transcribed?
- Promote binding of more regulators
- Recruit RNA pol
- Release RNA pol
- Release RNA from pause
Why might RNA polymerase pause? What needs to happen for it to move again?
It could get to another nucleosome. Activators need to come in to modify the nucleosome so that it can keep going.
Activator A causes one unit of transcription.
Activator B causes 2 units of transcription.
What could happen with activator (A+B)?
Way more (100 was the example). Two activators can have more than an additive effect
If an activator and repressor for the same regulatory sequence are present, what might happen?
They compete for binding
Binding site A is right next to B. A binds to an activator, B binds to a repressor. What could happen?
Repressor protein binds to activator protein, blocking it
If a strongly inhibiting protein binds to DNA, will transcription always be repressed?
No, there are multiple signal inputs that create a probability for transcription to happen
Why might transcription regulators be inactive?
Could be stuck in membrane, stuck outside nucleus, be bound to an inhibitor, have a subunit, be modified by phosphorylase, bound to a ligand, etc
If a transcription regulator is stuck to a membrane, could it bind DNA?
No
If mRNA is created by RNA polymerase, will it for sure turn into a protein?
Absolutely not, can be blocked at many stages before translation
How might mRNA decay once it’s transcribed on the 3’ end?
poly-A tail could shorten (what enzyme does this?)
How might mRNA decay once it’s transcribed on the 5’ end?
Decapping. This leads to rapid degradation of mRNA
What can deadenylase do if it binds?
Eat away the poly-A tail
If the poly-A tail is removed, will that always decay mRNA? why/why not?
No; poly-A polymerase exists in the cytoplasm that can bind and add them again
How does iron presence affect translation?
It can act BOTH as a ligand stops DNA transcription of one protein and starts transcription of another.
What does miRNA stand for? What does it do?
Micro-RNA. Regulates gene stability
How any types of miRNA are there?
400+
What’s the ‘argonaute’ protein and how does it relate to miRNA?
Binds with miRNA, then the complex cleaves some target RNA (???)
What’s ‘RISC’ stand for? What are its components?
‘RNA induced silencing complex’. Made of sliced up miRNA (sliced by Dicer protein) and Argonaute/etc.
What does the RISC complex do?
Fucks up mRNA
What does the RISC complex do?
Fucks up mRNA
What does ‘siRNA’ stand for?
Small interfering RNA
What is the function of RNA-dependent RNA polymerases in RNA interference (RNAi)?
They make more siRNAs to keep RNAi response going
What is the CRISPR locus?
A memory bacteria has of previous infections. DNA sequences of bacteria it acquired from previous infections
What is transcribed from the CRISPR locus? What is it bound to?
RNA is transcribed, then bound to Cas protein
What does the cRNA-Cas complex do?
Seeks out and destroys viral DNA sequences
What does the cRNA-Cas complex do?
Seeks out and destroys viral DNA sequences
What do operators do to operons?
Turn them off
What is the binding site for an activator protein called?
Enhancer
Take an E. Coli enhancer far away from the promoter. It gets a LOF mutation. Putting the normal enhancer on a plasmid doesn’t help. What does this imply?
The promoter is on the same chromosome as the LOF mutation. The DNA on it loops and (probably) binds to the mediator.
What happens when histone acetyltransferase binds to its transcription activator? (H3K9 is involved)
Binds to h3k9 (part of the histone tail) and acetylases a serine
What’s the idea behind histone acetyltransferase binding to an activator protein?
It starts a cascade that leads to chromatin remodeling complex coming on and transcription eventually starting up
If you add a poly-A tail to an mRNA in the cytoplasm, what’s a potential effect in regards to translation?
It can guarantee translation into protein (why? don’t know)
If you add a poly-A tail to an mRNA in the cytoplasm, what’s a potential effect in regards to translation?
It can guarantee translation into protein (why? don’t know)
What do transcription factors do?
They control the rate of transcription. Activator proteins and repressor proteins are both types of transcription factors.
What’s the essential difference between how activators/repressors act in prokaryotes vs eukaryotes?
Prokaryotes: act/repr directly affect polymerases
Eukaryotes: act/rep have many intermediary proteins (e.g. histones). Generally many regulators for one gene.
What are spacer DNA sequences?
e.g. junk DNA. Not in genes.
Is there a difference between ‘transcription factor’ and ‘general transcription factor’? If so, what is it?
Transcription factor: all activators and repressors. In both euk/prok
General transcription factor: Eukaryotes only. Bind at promoter to bring in RNA polymerase.
