Gene Expession Flashcards
Where do transcription factors bind to on small stretches of DNA?
The minor and major groove
How can gene transcription be activated at a distance?
DNA looping
What are the conserved signalling pathways?
Notch, wnt, hedgehog, TGFb family, RTK family
Why do cells have the same genes yet express different phenotypes?
they all have the same but are expressing different genes, i.e some of the genes re turned off some are on regulated by transcription factors
How are genes switched on?
activator proteins binding to the promoter region of a gene to begin transcription
What would happen to the lac operon gene in the following circumstances:
1. +glucose, +lactose
2. +glucose, -lactose
3. -glucose, -lactose
4. -glucose, +lactose
- operon is off, glucose is used as food source
- lac repressor binds, operon is off and glucose used as food source
- repressor is bound, activator is bound, operon is off
- activator is bound, operon is on, lactose can be used
What is a cis regulatory sequence?
a little bit of DNA where transcription factors bind, that’s on the sae molecule that the gene is on
what are examples of homeodomain proteins
hox genes, nanog and Pitx1
Where do homeotic mutations occur
in the homeodomain protein transcription factor
What is a helix-loop-helix protein and an example
made up of a short alpha helix connected by a loop to a second, longer alpha helix. binds as a dimer to interact with DNA. such as MyoD
Explain how the cis-regulatory sequences of the eve gene cause a stripe pattern
each of the 7 regulatory segments is responsible for one of the 7 stripes. such as eve stripe 2 - regulated by 2 activator proteins and 2 repressor proteins.
What is the difference in Pitx1 expression between marine and freshwater fish
Pitx1 expression results in a pelvic spine in stickleback fish, caused by changes in cis-regulatory sequences meaning that in freshwater fish, the TF cannot bind and the pelvic spine isn’t formed
Give the chain of events from an external signal to the result in developmental processes
external signal -> TF -> genes -> proteins -> cell properties -> developmental processes
What is the basis of the notch signalling pathway?
activated by ligand on neighbouring cells, contact-dependent, NOTCH receptor interacts with logan’s and some is cleaved off. moves to nucleus and targets CSL pathway. involved in lateral inhibition and somite formation
What is the basis of the Wnt signalling pathway?
binds to frizzled receptor, paracrine signalling, moves to nucleus, signalling prevents the degradation of beta catenin TF. when signalling is present the TF can enter the nucleus and alter transcription. used in limb development, tissue regeneration
What is the basis of hedgehog signalling?
binds to patched receptor, stops smoothened proteins working which translocates Ci protein to nucleus. with no hedgehog signalling, Ci is cleaved and repressed genes. involved in limb development, facial morphogenesis
What is the basis of the TGF beta family
extracellular TGF binds to receptors, activates SMAD proteins and phosporylates them to trans locate TF to nucleus. involved in bone formation and early vertebrate patterning
What is the basis of the RTK family
fibroblast and epidermal growth factors interact with RTKs which phosphorylase tyrosine residues, results in a cascade with phosphorylates the nuclear TF. maintains the mesoderm and involved in cell proliferation and limb patterning
What 3 mechanisms result in signalling specificity?
gene duplication, the response of the cell depending on the accumulation of other signals it recieves at the same time, cells with different TFs, proteins, RNA and chromatin states respond differently
What are the 2 mechanisms cells can use to maintain a differentiated state?
- autoactivated expression
- trithorax and polycomb groups stamping the chromatin to give a heritable record
What is the polycomb group responsible for?
structural development and stating what cells in certain locations will develop into. maintains hox gene repression/switching off genes
What is the trithorax group responsible for?
maintaining hox gene expression
What are the two types of chromatin
heterochromatin - condensed, restricts gene expression, inherited by daughter cells
euchromatin - looser
How is heterochromatin involved in early X chromosome development
one of the 2 X chromosomes is inactivated and becomes heterochromatin so will not express genes as TF’s cannot bind - therefore only 1 X chromosome will be expressing genes
What is the structure of chromatin
repeating nucleosome units (DNA helix wrapped around histones - histone tails can extend out from the core histones) with non-histone proteins attached. chromatin ins 30nm thread.
How can histone tails be modified
methylation, acetylation and phosphorylation - changes histones and DNA to express things differently. modification is reversible
How can chromatin be modified
changing the histone variant
How can TF’s cause changes in chromatin structure
nucleosome sliding, nucleosome removal, histone replacement and histone modification - all alter spaces for TF to bind more easily
How do embryonic stem cells remain in their state
by autoactivation and cross activation to maintain TF expression
