#28 Gene Regulation 10.24.12 Flashcards Preview

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Lecture objectives

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

2

What atre the 6 sites for gene expression control>

Transcriptional 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)

3

What kind of steps are invovled in gene expresison

Transcription, pre-mRNA processing, nuclear export, translation, and in some ases protein activiation (phosphoryation)

4

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

5

What is the best studied example of long noncoding mRNA and what is its function

Xist lncRNA

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
Silent transcription

6

What happens if you didn't silence one copy of X in females?

dose issue

7

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

8

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!

9

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

10

what does phosphorylation of GDP-bund eIF2 (inactive) do?

It traps eIF2in an inactive complex

11

What is the purpose of alternate splicing?

it allows for many different proteins to be translated form one gene

12

What kind of proteins control alternate splicing?

RNA binding proteins

13

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

14

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

15

Why are elements called "enhancers"

they can bind far from splice site that they are regulating

16

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

17

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)

18

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

19

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

20

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

21

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

22

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

23

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

24

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

25

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

26

What does C--> U deamination do in liver?

ApoB is an essential component of chyomicrons and VLDL

27

What does RNA editing do in the instestine, hwne it chages from CAA ocdon to UAA

resultsin a shorter protein that incorporates into chylomicrons

28

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

29

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)

30

What happens once decapping has taken place

Rapid 5' -->3' RNA degradation occurs. Likewise rapid degradation occurs at the 3' end