lecture 5 Flashcards
what makes one cell type different from another
what proteins are expressed in the cell (cuz every cell has same DNA + genome)
what specifically makes cells different from one another
transcriptional regulators
what leads to diff proteins being expressed
not all of the genes in DNA are actually transcribed/produced; some are turned off other are turned on
what’s the main idea of different cells
specific cell types are defined by proteins they express; some proteins are universally expressed, some are specific to each cell
why are cells different
all cells have exact same DNA and genes, but don’t have machinery to express the same genes
what dictates what proteins are expressed in cells
presence of regulators
what do Gs proteins lead to
generation of cyclic AMP and PKA activation
give example of how signaling can control gene transcription –> cell differentiation
active PKA enters nucleus where the DNA is; phosphorylates regulatory machinery that allows target gene to be expressed (in liver cell it wud be aminotransferase gene)
how much % of genes does typical human cell express
30-60%
what are 2 control points for regulating gene expression we focus on
transcriptional control, protein activity control (phosphorylation)
example of control of mRNA production thru transcription
transcriptional regulators
what do transcriptional regulators do
once activated, they scan DNA sequence in nucleus, look for specific nucleotide sequences upstream of gene they’re controlling that they can bind to
what 2 things can regulators do
activate or block gene transcription; either way you have unique gene expression
what regions of DNA do transcriptional regulators bind to
cis regulatory sequences
in other words what do transcription regulators do
scan DNA sequence, when it encounters part of DNA close to the gene its controlling, binds and provides docking site for machinery to allow production of messenger RNA
why is it ‘cis’ regulatory sequence
cis means close to mRNA sequences they’re gonna be transcribing / gene of interest
what can transcriptional regulators do to downstream gene transcription
either activate or repress
how do transcriptional regulators interact w/ DNA exclusively through
major grooves
why major and not minor grooves
b/c major grooves have more nucleotides for transcriptional regulators to interact with
what are all transcriptional regulators
dimers; always function as a pair
when scanning DNA for appropriate cis reg sequence to recognize (active/repress downstream gene), how do trans regulators do this
with 2 sets of protein-DNA binding regions
what is nanog
prefers T to C, next 2 must be A, next 2 prefers T to G, prefers G to A, equally C and G
what is the point of this nanog
cis sequence isn’t always gonna be identical; more wiggle room
if monomeric transcriptional regulator has no problem binding DNA sequence, then why do we have dimers?
dimers double amount of DNA needed to be recognized; like short vs long password
what does dimerizing allow
more specificity on where transcription regulators bind to a sequence; reduces chances that regulatory sequence is gonna be found in genome anywhere else BUT upstream of target
what is needed for DNA to be packed into nucleus
highly organized by being wrapped around histone proteins
what is the problem w/ histones
when DNA strand is wrapped around histone, it can hide cis reg sequence –> hinders ability of trans reg to get onto cis reg sequence
how does it deal with it
breathing and cooperative unbinding
what is breathing
1/20th of the time DNA is gonna naturally slip off the histone; once it falls off cis reg sequence is exposed and it binds
what happens once cis reg sequence falls of histone and binds to trans regulator
once it binds other machinery is recruited, histone is temporarily removed so mRNA can be regulated appropriately
what is cooperative unbinding
cis reg sequence is exposed, trans reg binds to it & recruits additional machinery to help remodel/reorganize histone-DNA complex, allows subsequent cis reg sequences to be exposed to allow additional trans regs to bind
describe breathing
kinda random, occasionally falls off, when cis sequence is on end of histone
describe cooperative unbinding
cis reg sequence is in center, multiple trans regs being recruited, more purposeful mechanism
tryptophan repressor
when enough tryptophan in cell, it binds to trans regulator binds to activate it, which binds onto cis-reg sequence and PREVENTS production of tryptophan
what activates trans reg
tryptophan
what happens when tryp activates trans reg which binds to cis reg sequence
RNA pol is blocked from accessing DNA when cis reg sequence is bound by trans reg
what is this an example of (tryptophan operon)
repressing the gene and preventing it from being transcribed
what happens if theres less tryptophan in cell
repressor remains inactive cuz there’s no tryptphan for it to bind
what happens if tryp doesn’t bind to trans reg
trans regulator isn’t activated and doesn’t bind to cis regulatory sequence which means RNA pol is free to bind cis reg sequence and produce more tryptophan
what else can transcriptional regulators do
activate transcription, not just repress
example of transcriptional regulators serving as activators
signaling molecule activates transcriptional regulator; binds cis reg sequence and actively recruits RNA pol rather than blocking it; allows messenger RNA to be produced
which is more complex mammalian or proks
mammalian cells have many more nodes of control; multiple cis reg sequences, multiple trans regs, etc.
how can reg sequences be 10k+ nucleotides away from gene of interest and still regulate the gene
because these things fold in 3D structure, putting them in close proximity
during development how are differences between one cell to another defined
defined exclusively by which transcriptional regulators are active
how many stripes of Eve protein
7
what are transcriptional regulators also known as
complex genetic switches
what are the 4 transcriptional regulators that control the regulatory segment in drosophila
bicoid, giant, hunchback, kruppel
how many regulatory sequences are in Eve gene DNA
7 regulatory segments (7 stripes)
within stripe 2 regulatory segment binding sites for how many transcriptional regulators
4; bicoid, giant, hunchback, kruppel
what are the transcriptional repressors in drosophila
giant and kruppel
what happens if giant and kruppel are active and bound to regulatory 2 stripe
they PREVENT expression of eve protein
what are the transcriptional activators in drosophila
bicoid and hunchback
where is eve protein gonna show up in
only cells that have BOTH of transcriptional activators and none of trans repressors
what is requirement to have stripe region
BOTH activators present (hunchback and bicoid) and both repressors absent (giant and kruppel)
sum up eve stripe
eve stripe 2 is under control of 4 transcriptional regulators; 2 repressors, 2 activators; it will only be expressed when both repressors aren’t there and both activators are there
what does combinatorial gene control do
creates hella diff cell types; diff combos of trans regulators give rise to many diff cell types [in daughter cells, one cell A has trans expressed other cell doesn’t, each of their daughter cells can have diff ones expressed]
just b/c transcriptional regulator is expressed doesn’t mean
it’s active
what is one way to activate transcriptional regulator
phosphorylation (covalent modification), ligand binding, etc.
transcriptional regulators are not just controlled by
protein expression; may need other things to activate it
what are 3 transcriptional regulators for fibroblasts
Oct4, Sox2, Klf4
what happens if you force fibroblast to express 3 trans regulators and allow them to grow
cells de-differentiate to stem cells and can become diff cell types
basically what do trans regulators do to cells
induce cells to differentiate
why are there only 3 trans regulators that do this
because they each control hella pathways and an enormous network of genes below theme [basically v small changes lead to v big effects]
what do trans regulators control
control cell phenotype
what do trans regulators recognize & bind to
recognize nucleotide sequences, bind to major groove on DNA
what can trans regulators do to downstream genes
can activate or repress downstream genes
a single euk gene is controlled by how many regulatosr
10s-100s
what can this complexity in regulation allow for
protein expression at right place and time during dveelopment
what can right combo of transcription factors do
reprogram cell fate
