Flashcards in #28 Gene Regulation 10.24.12 Deck (65)
1. Describe how RNA editing, mRNA decay or by altering either the start site, splicing or 3" processing affets teh protein product
2. Describe the different strategies of translational control (pay attention to molecular basis by which RIBOSWITCHES< IRESs, miRNAs and RNAis work)
3. Describe th role of miR-21 in cancer
What atre the 6 sites for gene expression control>
RNA processing conrol
RNA transport and localization control
Translation Control (
mRNA degradation control
Protein activity control (covalent modification or by complex formation with another protein or small ligand)
What kind of steps are invovled in gene expresison
Transcription, pre-mRNA processing, nuclear export, translation, and in some ases protein activiation (phosphoryation)
what are long noncoding RNA (lncRNA)? how many more lncmRNA are transcribed than mRNA? What is the funciton?
>200 nts long
10-20x more of the nts in the genome are transcribed as lncRNA than as mRNA
Expected to play a KEY ROLE in regualtion of gene expression
What is the best studied example of long noncoding mRNA and what is its function
essential for inativation of one copy of the X chromosome in females
This lncRNA "coats" this chromosome
Recruits histone remodeling complex
Trimethyates specific histone lysine
What happens if you didn't silence one copy of X in females?
What is the point of "Leaky scanning" ( variety of either using first AUG or later AUG as start site) to initiate translation
allows there to be a control of signal sequences for the protein ,providing control of where in teh cell a protein is located
How is guanine nucletoide ehsange factor employed in normal translation
Guanine nucleotide exchange factor (eIF2B) recycles GDP in eIF2 after translocation. This exhcange saps GDP for GTP, transforming inative eIF2 to active form!
How is "leaky scanning" employed during STARVATION
during amino acid starvation, protein kinase Phosphorylates the GDP formm of eIF2-->becomes trapped in an INACTIVE COMPLEX with eIF2B
This dramaticaly SLOWS down tranlsation ,thereby increasing the likelihood that a later AUG will be used for translational initiation
what does phosphorylation of GDP-bund eIF2 (inactive) do?
It traps eIF2in an inactive complex
What is the purpose of alternate splicing?
it allows for many different proteins to be translated form one gene
What kind of proteins control alternate splicing?
RNA binding proteins
How does negative control regulate alternative splicing?
repressor molecule binds to a splice junction. Binding of repressor portins sometimes uries the splice site, maksing it so that splicing mahcinery doens't recognize th splice site
How does positive control regualte alternative splicing
bindign of splicing activotro to an ENHANCER ELEMENT can recruit th splciing machiney to a poorly defiend splice site
Why are elements called "enhancers"
they can bind far from splice site that they are regulating
How can alternate 3' cleavage of the message lead to two different forms of an anitbody?
one that is secreted and anotehr that is membrane bound
Describe the membrane bound antibod formation
Membrane bound contains C-terminal Hphobic region and occurs in unstibmulated B lymphocytes
inron containing a PREMATURE STOP CODON has been spliced out and the full length protein is made (Antibody bound to membrane)
Describe formation of stimulated B lymphocyte that are not bound to membrane
Expression is incresed for a subunit of FstF (cleavage stimulator factor).
As a result of this higher concetnration, an earlier 3' cleavge site on the pre-mRNA is recognied and it is cleaved inside the intron and then polyadenylated.
This second form of hte antibod is shorter and b/c it is missing the hphobic tail f the full-lenght protein, it is secreted
What is CstF and function?
it is cleavage stimulator factor
Higher concentration of cleavage stimulator factor leads to an earlier3 cleavage site on the pre-mRNA is recognized and is cleaved INSIDE the INTRON and then polyadenylated
2nd form of antibody is shorter and b/c it is shorter and b/c it is missing the Hphobic tail of the full-length protein
What is RNA editing? When does it happen
process that occurs after transcription and thus modifies the resulting translated protein sequence
ADAR's chnage A--> I
There can also b editing in splicing
What are ADARs?
Adenosome Deaminases acting on RNAs-
estimated to carry our A--> I (adenosien to inosine) editing in over 1,000 different human genes
How does A--> I change the translated protein? What is the complementary base of I?
A usually pairs with U
I is like G and pairs with C
I pairs with C
Does ADAR recognize ss or ds RNA?
DS RA to b editted and its complement
The edited sequenc eis foten int ehe xon region with the complementoary region in the intron, near the 3' inron jucntion
There is a transmitter gated ion channel in teh brain that changes A to I. TWht does this do>
it causes Gln--> Arg mutation ,that alterst ehh claciumpermeability in the channel
What type of RNA editing is involvd with changing C-->U (in liver>)
What aobut in intestine? for ApoB-28
C is daminated to U
releavant example with two forms of ApoB protein
in the liver ApoB-100 is an essential component of chylomicrons and VLDL (NO EDITING..it is CAA)
Om omtestome. CAA Gln codon is edited to a UAA stop codon, resulting in shorter ApoB-48 protein that incorporates into chylomicrons
What does C--> U deamination do in liver?
ApoB is an essential component of chyomicrons and VLDL
What does RNA editing do in the instestine, hwne it chages from CAA ocdon to UAA
resultsin a shorter protein that incorporates into chylomicrons
Which mRNA is more stable? Bacterial or Eukaryotic?
Bacterial . Most bacterial mRNA is made quickly and degraded quicky, allowing these simple orgnaism to adapt rapidly to their ever changing environment . A typical bacterial mRNA has a half-life of about a minute or two
Euk mRNAas halve a typical half life of 3- minutes but soem last up tot 10 hours
How many nucleotides at the tail ends until degradation beins at both end?
25 nucleotides in humans
3'Poly A tail is gradually shortened
5' Cap (decapping)