Regulation of Gene Expression Flashcards
What distinguishes higher organisms isn’t a difference of genes, but rather a difference in the …
regulation of genes
Because all nucleated cells contain the same DNA, the difference in cell phenotype must be based on _______
differential regulation of gene expression
Think of 6 ways eukaryotic gene expression can be controlled.
1) DNA structure
2) Frequency
3) Splicing
4) where mRNAs go
5) which mRNAs are translated
6) rate of mRNA degredation
7) control of proteins
Just know that increasing the number of gene copies can increase expression. More copies, more expression.
Gene Copy Number
Euchromatin __________
Transcriptionally active; loose chromatin
Heterochromatin____________
compact chromatin (SILENCING genes), transcriptionally inactive
Acetylation of Histones=
euchromatin, active transcription
Deacetylation of histones=
Heterochromatin, inactive transcription
Regulatory regions near transcription initiation contain short stretches of DNA called ______ and gene regulatory proteins, _______, that recognize and bind to these stretches for gene regulation
DNA- cis-acting
protein- trans-acting
The _____ groove of the DNA helix is accessible for regulatory proteins to bind to for regulation
Major
*** proteins can bend DNA and change the structure of DNA for gene regulatioin
Gene regulatory proteins contain specific structural motifs that recognize DNA sequences. Numerous contacts are made to ensure that the interaction between protein and DNA is strong.
Cool.
Motif __________ is one of the most simplest and common motifs.
Helix-turn-helix
Motif– _________ proteins are a special subclass of helix-turn-helix proteins that are key Regulators of animal development (embryonic)
Homeodomain proteins
***** important
Motif- another important group of regulatory proteins is ________ proteins because they have zinc atoms and they look like fingers.
Zinc Finger Motif…..pretty obvious
Motif- This dimer grips DNA like a clothespin on a clothesline. It’s called the _______ motif
Leucine Zipper
Motif– _______ motifs can create both homodimers and heterodimes
Helix-Loop-Helix
Many regulatory proteins can bind as heterodimers. Heterodimerization increases….
the variety of DNA sequences recognized
In bacteria, gene switches allow for the expression of genes to be dependent on the available food in the environment. “Gene switches in action”.
Awesome.
Explain the E.Coli tryptophan operator. ie. What happens when tryptophan is present in the cells environment?
- the 5 genes needed to produce tryptophan are next to each other and are controlled by one operator
- when tryptophan is present in environment, expression of 5 genes no longer needed–> production needs to be shut off
- tryptophan activates tryptophan repressor protein which attaches to the operator, blocking the binding of the promoter
- NEGATIVE CONTROL
Activator proteins can ….
assist in the binding of RNA poly to help promote transcription
Negative regulation:
bound repressor protein prevents transcription
Positive regulation:
bound activator protein promotes transcription
______can bind regulatory protein to remove it from DNA or bind to allow regulatory protein to bind to DNA– for both repressor protein or activator protein
ligands
Go study lac operon
Quick quesiton: what if there was a mutation of the enzyme that converts Lactose into Allolactose…?
Regulation in eukaryotes is very complex. Regulatory regions can be very long, and unlike prokaryotes, RNA poly cannot initiate transcription on its own; it must have __________ proteins that assemble at the promoter for transcription to occur
basal transcription factor proteins
Regulatory sites that are distant from the promoter are called ______. These sequences loop to join the promoter
enhancers
***can also repress
Many gene regulatory proteins consist of two domains: a _____ that recognizes specific DNA and an _____ that accelerates transcription
structural motif; activation domain
Transcriptional synergy:
multiple activators can have a greater than additive effect on gene transcription
Don’t forget how important opening and closing chromatin is for gene regulation. Histone acetylases and histone deacetlyases…..
Acetlyation opens=transcription active
Deacetylation closes= transcription inactive
Competitive DNA binding: gene ____ proteins can compete with gene activator proteins for the same regulatory DNA sequence.
Gene Repressor Proteins
Masking the activation surface: repressor proteins can….
bind the activation site of the activator protein thereby preventing activation of transcription
Direct interaction with the general transcription factors: the repressor blocks assembly of the….
general transcription factors
Recruitment of chromatin remodeling complexes: repressor proteins recruit chromatin remodeling proteins which essentially…
closes up the DNA, silencing the promoter
Recruitment of histone deacetylases: the repressor attracts histone deacetylases to the ______
promoter
gene regulatory proteins often assemble into complexes on DNA. An example is the ______; a group of proteins that form together on an enhancer to regulate transcription at a distant site
Enhanceosome
Insulators are….
DNA sequences that prevent regulatory proteins from influencing distant genes (like non related genes)
Insulator sequences both prevent the spread of ______ and directionally block the action of _____
heterochromatin; enhancers
An example of a gene that would be coordinated by a single protein is ________
human glucacorticoid receptor protein, which makes things like cortisol
*** Rapid change wanted in gene expression
Chromosome-wide alterations in chromatin structure ( and ultimately gene expression) can be _____
inherited
Epigenetics is defined as ________, ________ changes in the genome (no changes in the sequence) that regulate gene expression, most often resulting in _______. It can be influenced by the environment
heritable, reversible; gene silencing
_______is a classic example of epigenetics, which is involved in imprinting, development, X-inactivation, and diseases
DNA methylation
Explain X inactivation
Female= 2X chromosome
only one can be active, the other becomes bar-body of heterochromatin–>silenced chromosomes<– which is mediated by noncoding RNA called XIST
What are four mechanisms that produce epigenetic form of inheritance:
1- positive feedback
2- histone modification (production of heterochromatin)
3- DNA methylation —leads to heterochromatin
4- Protein aggregation state, conformational change to aggregate state
The inactivation of the X chromosome in inherited, meaning…
the progeny cells of the early embryo will have the same X silenced –> clonal inheritance
The “5th most common base” is _______.
When something gets methylated, it is maintained in progeny cells of replication.
5-methylcytosine
Imprinting is differential expression of gene allele depending on _________
parental origin
The purpose of imprinting is to control….
gene dosage= only one allele is expressed as the other allele is imprinted and silent
Imprint is created in the _______ cells
parental germ cells
***paternal or maternal
The mechanism of gene silencing for imprinting is….which leads to….
5-cytosine DNA methylation which leads to chromatin condenstation
Read through mouse slides about imprinting….Male sticks with male, female with female?
ok.
Silencing of tumor suppressor genes is common in cancer. Think about it.
Tumor suppressor gene methylated probably….heterochromatin…silenced….gene doesn’t express tumor suppressor protein.
Transcription of genes can be increased by extracellular signals that induce signal transduction cascades. Examples:
hormones
growth factors
Splicing can be regulated by ____, _____, _____ and _______
tissue
stage of development
age
disease
Abnormal splicing of mRNA can give rise to proteins with oncogenic properities
bummer
Gene expression can be regulated by nuclear transport. How is that?
mRNA is regulated by signal-mediated transport through the nuclear pore grated channel
-only fully processed mRNAS can be transported
The ____ protein of HIV transports unspliced HIV mRNA from nucleus to cytoplasm, skipping regulation by nuclear transportation
Rev Protein
The amount of mRNA in the cell is due to ____ and ____ of mRNA
the rates of synthesis and decay
To control the amount of mRNA, the _______ can be tightly regulated. Increase ______, decrease mRNA, decrease expression.
rate of degradation for both blanks
Two ways metabolism is regulated in cells:
1- amount of DNA
2- amount of protein translated
If there’s a question about antisense mRNAS just pick answer with …..
circadian clock
_______ and _____ are short RNAs that are used to silence viral gene expression
microRNA and short interfering RNA (siRNA)
Low iron (Fe) requires that cell to shut off _____
Ferritin production
Ferritin does what?
Ferritin binds and sequesters intracellular iron. Therefore in a low Fe state, ferritin would need to be shut off
in state of low Fe, Ferritin is inhibited by..
IRE-BP protein that inhibits ferritin translation
Transferrin receptors do what?
import iron across the plasma membrane of a cell
Ferritin and Transferrin are both mediated by the same iron-responsive regulatory protein _____ , that dissociates from mRNA when it binds Fe.
Aconitase
***** but both ferritin and transferrin are regulated differently
Binding of aconitase to the 5’ end of ferritin receptor mRNA blocks…..
So:
-Fe starvation
-Fe excess
blocks translation initiaiton
Fe starvation: not bound by Fe so translation blocked, therefore ferritin can’t sequester Fe
Fe excess: Fe binds aconitase, releasing it from ferritin hair loop, allowing for translation of ferritin gene–Fe going to be sequestered
Binding of aconitase to the 3’ end of transferrin receptor mRNA….
- Fe starvation
- Fe excess
… stabilizes mRNA by preventing endonucleases from cleaving/degrading mRNA
- Fe starvation: aconitase binds mRNA hairpin, allowing for Transferrin translation–> uptake of Fe into cell
- Fe excess: aconitase bound by Fe, released from mRNA, leaving hairpin free for degredation –> transferrin receptor gene not translated
glycosylation:
addition of a carbohydrate to protein
phosphorylation:
kinases add proteins to make them active/inactive
dephosphorylation: removes p (phosphatases)
Lipid modification:
addition of lipid to protein
Cleavage of protein:
unmasks functional group of protein
Circadian clock runs on 24 hour clock that….
produces Tim and Per proteins that repress own transcription in nucleus on 24 hours cycle. Light degrades Tim
you can also degrade and allosterically regulated proteins
Last card.
