exam 2 control of gene expression: regulation of mRNA levels Flashcards
how do cells respond to environmental changes
cells must be able to control the timing and level of gene expression in a dynamic fashion
where does a major component of gene expression regulation occur at
the level of mRNA expression - the first place where regulation can occur
what levels can mRNA be regulated at
transcriptional initiation, elongation, splicing, nuclear export, degradation
where does the best understood mechanism of regulation occur at
transcriptional initiation, and involves combinatorial control by transcription factors
what key roles do calcium ions have in cell activities
muscle contraction, cell division, secretion, endocytosis, fertilization, synaptic transmission, metabolism, cell movement
where can gene expression be regulated at
essentially every step from transcription through protein activity/stability:
- transcription from DNA to RNA
- splicing, RNA tail, 5’-cap addition
- where RNA goes in cytoplasm
- mRNA degradation and control
- translation steps and initiation
- protein activity control
- protein degradation
where does the primary regulation of genes occur at
the level of RNA transcription - matching RNA synthesis to expression requirements avoids being very energetically costly
what are gene regulatory proteins/transcription factors
sequence-specific DNA-binding proteins that play a key role in defining the level of transcription
what do transcription factors contain
one or more of a small set of well-characterized DNA-binding motifs
what can transcription factors bind to and read
the outside of the DNA helix and influence the binding or activity of RNA polymerase II
what are the two accesses DNA has to being able to see bases
major groove and minor groove
where do most TF factors bind
major group because there is more info in the major groove than minor groove
what is different about the major groove
it’s not symmetrical = you can tell where bases are and which strand you are examining
what do the major and minor groove represent
opposite faces of a base pair
what’s the difference between major and minor groove
- each base on a strand can be distinguished in the major groove
- only AT base-pairs and GC base-pairs can be distinguished in the minor groove
what can a DNA-binding protein interact with
specific base pairs without unzipping DNA
what can occur through hydrogen bonding
interactions between the gene regulatory protein and a base-pair can occur
how many contacts are made by a gene regulator protein with DNA
10-20
what is the helix-turn-helix DNA binding motif
two alpha helices connected by a short unstructured stretch (“turn”) - helices are held at a specific angle by interactions between the helices
what does the C-terminal recognition helix of the helix-turn-helix motif make
sequence-specific contacts in the major groove of DNA and bind to DNA as symmetric dimers
what are symmetric dimers
two proteins are structurally similar and bind as mirror images
what happens with symmetric dimers
recognition helices bind to “half-sites” separated by one turn of the DNA helix on the same face of DNA
what does heterodimerization allow for
expansion of sequences recognized without expanding number of proteins made
where does the major groove fit in
the alpha helix
what is the homeodomain
a special case of helix-turn-helix motif
what is the structure of the homeodomain
a larger structure of helix-turn-helix plus third alpha helix
what does the conserved structure of the homeodomain suggest
all homeodomains are presented to DNA in the same fashion
what is the zinc fingers DNA binding motif
one or more zinc ions (prosthetic group) is coordinated by amino acid side groups
what does one subclass of zinc fingers use
2 cysteines and 2 histidines to coordinate zinc between an alpha heliz and a 2-strand antiparallel beta sheet
where are zinc fingers usually found
in tandem clusters with a DNA-binding protein
what does a series of zinc fingers allow for
sequence specificity because each finger recognizes one or two base pairs
what does the second subclass of zinc fingers use
coordinates 2 zinc ions using 4 cysteines for each
- one zinc ion stabilizes a recognition helix and one stabilizes a loop involved in dimerization
what do zinc fingers bind to
DNA as symmetric dimers, similar to helix-turn-helix proteins
what is the leucine zipper motif
alpha helix containing a hydrophobic surface on one side
what do hydrophobic forces do to the leucine zipper
keeps lucines away from water and drives binding of two subunits together
what do proteins bind DNA as
as a dimeric structure
what happens with leucine zippers
the helix from one subunit binds to the corresponding helix in the second subunit in a coiled-coil structure - hydrophobic interactions
what does an alpha helix do in a leucine zipper
serves as both the dimerization region and the DNA-binding region
what is the helix-loop-helix binding motif
similar to helix-turn-helix but with a longer loop of proteins that connect to helices
what happens with helix-loop-helix structure
a short alpha helix is connected to a longer alpha helix by a flexible loop, which allows one helix to fold back and pack against the other
what does the helix-loop-helix structure act as
both a dimerization interface and the DNA-binding region, like with leucine zipper
what can dimerization of DNA-binding proteins enhance
binding and specificity by increasing the contact area with DNA
what does heterodimerization increase
the range of sequences that can be recognized
how many different sequences could be recognized by dimerization of a TF that has 3 different pairing partners, A B and C
6 - hetero and homodimerization
what are the two types of gene regulatory regions transcription factors generally act at
promoter or enhancer
what is the promoter
the region where RNA polymerase and the general transcription factors assemble
where is the promoter located
a short distance upstream of the 5’ end of the gene
what is specific about a promoter
it is gene-specific and orientation is important
what is the enhancer
an independent region outside promoter
where is the enhancer located
very far away from the promoter and may be upstream, downstream, or within the gene
what can the enhancer region not drive on its own
transcription, but can increase it from its corresponding promoter
what is not specific about enhancers
they are position and orientation INDEPENDENT and can work with a promoter of a different gene (heterologous)
how are eukaryotic gene regulatory regions different than prokaryotic
they’re more complex
what is combinatorial control of expression
multiple gene regulatory proteins work together to control the rate of transcription
how do TFs work cooperatively
two activators - increase transcription synergistically
how do TFs work antagonistically
an activator vs a repressor
what can combined use of repressors and activators enable
sophisticated control of transcription in bacteria - activator is only present in absence of glucose
what can TFs help to unpack*****
chromatin, making the gene accessible to RNA polymerase and the initiation complex
what can TFs control*****
recruitment of RNA polymerase and/or general TFs to the promoter
what can TFs regulate*****
the switch from initiation to elongation
what can TFs help recruit*****
histone-modifying enzymes to change the local chromatin structure
what can TFs bend*****
DNA to allow long-distance interactions between gene regulatory regions
can transcription factors serve as activators or repressors
both
what can transcription activators direct
local alterations in chromatin structure
why are TF selectively activated
cannot have every TF turned on in cells at all times
where are TFs regulated at
level of gene transcription - if not, must be regulated post-transcriptionally
what are TFs activated by
phosphorylation - MAPK family helps with this in response to signals from cell-surface receptors
