exam 2 control of gene expression PT regulation Flashcards
what can small non-coding RNAs do
regulate gene expression
what PTMs regulate protein function
activation/de-activation, co-localization with interacting molecules, assembly into multi-protein complexes
what can protein level be regulated by
ubiquitin/proteasome-mediated degradation
what does phosphorylation do
converts an inactive form into an active form and vice versa
what are molecular integraors
transcription factors have multiple sites for phosphorylation and other modifications
is the GTP-bound form activated or inactivated
activated
what does Ras do
phosphorylates and activates first kinase in cascade, which amplifies signal
what does the final map kinase do
prosphorylates Elk, which induces transcription and moves into nucleus to continue kinase cascade of phosphorylating things on and on
how do PTM regulate TF activity
changes cellular localization
what are the varsity of TFs
NF-AT and NF-kappaB
what happens with NF-AT and NF-kappaB
regulated by localization: held in cytosol inactive, then PTMs lead release and translocation to nucleus, where nuclear TF is able to regulate gene transcription
what is the self-regulating TF
NF-kappaB - induces transcription once in nucleus
what can combinatorial control generate
patterns during animal development
what is even-skipped expression
even segments are all missing when mutated - expression in one stripe is directed by one DNA molecule
what are positive transcription factors
where gene is expressed
what are negative transcription factors
boundaries of expression
how do different cell types arise to be able to express different TF patterns
- cells in different places in an embryo can sense their locations and activate/express different TFs
- during development, cells can receive different soluble signals that direct TF expression/activation
where can RNA levels be regulated at
level of initiation or termination
what does transcriptional attenuation lead to
premature termination of the RNA transcript
what does a growing RNA chain adopt through transcriptional attenuation
conformation that interferes with RNA polymerase activity - RNA pol pauses and aborts transcription
how can transcriptional attenuation be reversed
by binding of specific proteins to the RNA structure, allowing RNA pol to complete transcription
what are most eukaryotic genes regulated by
alternative splicing
what are splice variants
a gene with even just a few exons can produce many different mRNAs via alternative splicing
how does HIV use regulated nuclear export
to allow RNA molecules containing some introns to be exported from the nucleus
how can cells use regulated cytosolic localization
to place specific mRNAs at specific locations in the cell, allowing mRNAs and encoded proteins to be concentrated in a particular part of the cell
how are genes regulated by mRNA stability
mRNA is rapidly degraded under certain conditions
what does aconitase do
iron-binding protein
what does endonuclease do
cleaves RNA, leading to degradation = no transferrin made
what happens with high levels of iron
want ferritin, don’t want transferrin
what happens with low levels of iron
want more transferrin and no ferritin
what is ferritin
binds to iron in cell to keep it protected
what is transferrin
imports iron in cell
what forms the RNA-induced silencing complex (RISC)
a short double-stranded RNA is generated after processing and associates with a set of proteins
what do miRNAs fold into
hairpin stem-loop structures
what happens with the hairpin structure
one strand of RNA is degraded and the other makes base-pairing contacts with an mRNA target
what does dicer do
cleaves off loop part of hairpin structure
once RNA is sliced, how is it unstable and rapidly degrading
one half has 5’-cap, no poly-A tail and vice versa
what do siRNAs do
mediate the process of RNA interference
how is dsRNAs formed
formed by base-pairing between complementary regions of separate RNA strands
what does dsRNA do
cleaved by dicer nuclease to form siRNA
what does siRNA associate with
proteins to form RISC, and target mRNAs are cleaved
how does siRNA form RITS complex
associated with different set of proteins
what is the RITS complex
inhibits gene transcription by modifying chromatin structure
what is dsRNA recognized by
dicer complex and is used to cut up siRNAs to form RITS
what advantages might come from post-transcriptional regulation
can respond to environmental stimuli more rapidly than transcriptional regulation
- have protein - can quickly turn it on and off when you need it
what can info in the 5’ and 3’ untranslated regions (UTRs) regulate
translation efficiency and mRNA stability
what blocks ribosome access
5’ UTR RNA structure
what inhibits ribosome scanning
RNA structure
what can switch translation on and off
riboswitch structure using binding of an ion or small molecule
what is required for efficient translation initation
repressors binding to 3’ UTR can prevent communication between 5’ and 3’ ends of mRNA
what can phosphorylation of initiation factor eIF2 do
inhibit global protein synthesis by activating eIF2B, a translation initiation inhibitor
what does eIF2 use
GTPase motif to mediate binding of initiator met-tRNA to small ribosomal subunit
what is eIF2B
GEF that catalyzes exchange of GDP to GTP, activating eIF2
what happens in absence of active eIF2B
excess eIF2 remins in its inactive, GDP-bound form and protein synthesis slows dramatically
what does IRES (internal ribosome entry sites) allow for
ribosomes to skip the first AUG, which allows two different protein sequences to be derived from a single mRNA
what is required for secreted/transmembrane proteins
different initiation sites leading to skipping of signal sequence, switching between cytosolic and secreted form of a protein
what allows for independent simultaneous translation of two completely different proteins from one mRNA
IRES sitting between two separate ORFs
what is protein turnover
another point of regulation
why must damaged/mis-folded proteins be destroyed
to prevent accumulation of malfunctioning proteins
what does ubiquitin/proteasome system allow for
regulated destruction of proteins
- targeted protein is polyubiquitylated
- proteasome recognizes polyubiquitylated protein and degrades it into short peptides
