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
