Translation II

Question 1

How can you regulate/alter translation?

Answer 1

1. ) Regulation by varying the mRNA structure and sequence
2. ) By altering the fx. of initiation factors
3. ) By protein binding to the mRNA

Other mechanisms: modification of rib, ribosome shunting and hopping, protein cleavage during translation, and codon redefinition

Question 2

By varying mRNA structure and sequence

Answer 2

a. ) Having an mRNA that gives rise to the same protein, but uses a more rare tRNA. Slows production.
b. ) Upstream structures from start codon that inhibit ribosome scanning (eukaryotes) or occlude the Shine Dalgano sequence (bacteria). DECREASES rate of initiation.
c. ) Diff start codons have diff strengths depending on their kodak content. AUGs with weak kodak can be bypassed so downstream ones are used. Result is 2 diff proteins produced at certain amts from the same mRNA
d. ) Frameshifting b/c a specific RNA seq and structure in the middle of the coding part of the RNA results in the ribs slipping into a different reading frame a certain part of the time (recoding)
e. ) IRES RNAs can drive cap-independ pathway of rib recruitment and initiation in eukaryotes. Fx. of IRES can be modulated based on cellular conditions, and are probably imp for regulating gene expression.
f. ) RNA editing- transcribed mRNA is modified specifically in such a way that the coding is affected. This can be tissue specific, so the same gene encoded in DNA can be used to produce 2 diff proteins (apoB is example).

Question 3

Altering fx. of initiation factors (eIF4E)

Answer 3

eIF4E (cap binding protein for initiation) can be bound by 4E-BPs that sequester and block its fx.
When BPs are phosphorylated, do not bind 4E… so you get cap-dependent translation initiation.
But under stress, bps are dephos, bind 4E and block fx.

Can also be induced by rapamycin. Get shut-down of translation. (but some msgs still translated, like IRES-containing ones).

Question 4

Altering fx. of initiation factors (eIF2-alpha)

Answer 4

eIF2-alpha is critical for steps that lead to binding of the initiation tRNA to the ribosome.
when its phosphorylated its activity in inhibited, initiation blocked.
how get phosphorylated? by interferon (produced when cell infected by virus) so shut down of translation is response to viral infection
Other cell stresses lead to its phosphorylation.

Question 5

Regulation by protein binding to mRNA

Answer 5

3’ and 5’ UTRs of eukaryotic mRNAs are full of sites that can be bound by specific proteins. Can affect everything from mRNA stability, localization of mRNA, degree to which ribs bind, etc.

Also, presence/absence/length of the poly-A tail on the extreme 3’ end of the RNA can affect the degree to which it is translated, presumably because of protein binding. During oocyte maturation, mRNAs with short poly-A tails are inherited from mother but are quiet. AT right time in development tails grow and become active.

A good example of protein binding to specific structures in mRNA is iron metabolism. Mechanism involves protein binding specific mRNAs and changes binding pattern that occur when iron levels change.

Question 6

Iron

Answer 6

Transferring binds iron, Transferrin receptor (TFR) brings transferring/Fe into the cell, ferritin sequesters excess Fe,

iron response element (IRE): RNA stem-loop structure in mRNA’s that can bind IRP
Iron response bp’s: bind Fe and regulate expression of ferritin and TFR.

High fe: IRe-bp’s bind to fe and can’t bind ire-rna

low fe: ire bp is NOT bound to Fe, so it CAN BIND ire-RNA, so mRNA is protected from degradation. Transferrin receptor synthesis continues.