Lecture 17: Gene Regulation Flashcards
What do txn reg proteins have in common?
usually contain recognition alpha-helix, which inserts into the major groove of DNA and makes multiple contacts
What kind of interactions determine DNA site recognition? What kind of bonds are predominantly formed?
AA-base pair interactions
H-bonds
What is the repressor molecule in the Trp operon? Where does it bind?
Trp
Operator
Where is the operator in an operon located?
Within promoter
What is an operon? What kingdom has this?
clustered genes, coordinately regulated
To what sequence does a repressor protein in an operon bind?
operator
What does polycistronic mean? Where is this found?
multiple distinct proteins can be made from single mRNA
bacteria operon
The operator is a ____-acting sequence in an operon
cis
what is constitutive expression?
only transcribed when needed
Txn factors are modular. What does this mean? What is the result?
DNA binding domain can bind independetly of repressor/activator domain
novel activity
How does txn factor modularity result in novel activity?
can have fusion of different parts with different txn factors
ex. xs translocation
Euk txn regulators bind ______ and stimulate ______
enhancers
RNA Pol II
How can aeukaryotic enhancer be far away from a promoter, but still affect txn?
looping
What three molecules must bind to activate euk txn?
txn factors (activator protein)
Mediator
Rna Pol
activators in eukaryotic txn acts through ______ to recruit ______, and can also recruit ______ modifying enzymes
intermediary proteins ex. mediator complex
Rna Pol complex
Chromatin
Where do euk enhancers work? What allows this to happen?
upstream, downstream, or within gene
looping
What does overexpression of HOX11 gene cause? What is HOX11?
T-cell actue lymphoblast leukemia
T-cell gene enhancer
What needs to happen to chromatin before txn can occur?
needs to loosen up
what two major types of chromatin modifications can be done to loosen chromatin and allow txn?
- covalent histone modifications
2. ATP-dependent nucleosome remodeling (move, slide, exchange)
what does acetylation of a histone do?
activate txn
What does de-acetylation of a histone do?
repress txn
What are the 4 possible histone modifications? What structures are modified?
Residues are modified
acetylation/de-acetylation
methylation
phosphorylation
What are the 2 ways in which euk gene activator proteins increase the rate of txn initiation?
- act directly on txn machinery
2. change local chromatin structure
What do histone acetyltransferases (HATs) do? What do histone deacetylases (HDACs) do?
HAT - hyperacetylate chromatin (activate gene exp)
HDAC - hypoacetylate chromatin (deactivate gene exp)
what is steroid receptor (glucocorticoid receptor - GR)? does it act on one or multiple genes?
txn factor
multiple genes
The fact that each regulator targets multiple genes can be the root cause of _______
drug side effects
What are 7 activities which regulate synthesis and activity of txn factors?
- protein synthesis (feedback)
- ligand binding
- covalent modifications (phos)
- add’n of 2nd subunit
- unmasking - remove something
- stimulation of nuclear entry - remove inhibitory protein, can enter nucleus
- release from membrane
What underlies the development of different cell types? What can happen when this doesn’t happen successfully?
exp of different txn factors
cancer
What is gene expression profiling? What techniques does it use? what is the clinical use?
- measures abundance of mRNA in cells or tissues
- DNA microarray, RNA seq, cluster analysis
- link expression patterns to clinical outcomes, pharm effects
What is the Hb tetramer composed of?
2 alpha, 2 beta subunits
What are the only 3 places where Beta globin is produced?
adults
bone marrow
erythroid cells
What is the locus of control region? What does it do?
shared control region for ALL beta globin like genes in a cluster
How does the beta globin gene cluster differ in different cells?
euchromatin where expressed
heterochromatin in cells where not expressed
What is the result of deletion of the locus of control region?
silences entire cluster for beta globin production
beta thalassemia = severe anemia
What is the cell memory mechanism of autoregulation?
txn factor activates its own gene in add’n to other genes
What happens in the cell memory epigenetic mechanism of modification of histones?
acetylated or methylated state of chromatin is passed from parental cell to daughter cells
keeps genes expressed at similar levels across cell generations
What happens in the cell memory epigenetic mechanism of modification of DNA?
methylated DNA attracts histone modifiers
leads to txn repression
