BCH 5413 - EXAM 3, MODULE 1 UPDATED ACTUAL
QUESTIONS AND CORRECT ANSWERS
Question:
1. Do all mRNA have the same steady state concentration?
Why or why not?
Answer:
No. The steady state concentration is dependent on the rate of synthesis and the
rate of degradation. For example, ribosomal proteins are always needed and
therefore have much more stable mRNAs so the proteins can be consistently
made. However, cytokines are condition dependent and are only needed under
certain conditions. Therefore, their mRNA is less stable because the proteins are
only needed conditionally.
Question:
2. Deadenylation of an mRNA results in the loss of the
polyA binding protein. What role does this play in
facilitating mRNA degradation?
Answer:
De-adenylation of mRNA by the deadenylase complex begins at the 3' end of the
poly-A tail and removes the A residues until the poly-A tail is removed. This results
in a loss of the PABP (normally bound to poly-A and eIF4G to prevent
degradation), which is a key protein to the circularization of the mRNA. When the
3' end is exposed, the exosome can come in and degrade the mRNA in the 3' to 5'
direction. Alternatively, after the poly-A tail is removed, the mRNA can be de-
capped (via DCP1/DCP2) then degraded from the 5' to 3' end using XRN1
(predominant pathway in yeast but not mammals).
Question:
3. What is the significance of the ARE (AU-rich elements)
found in the 3' non-translated region (NTR) of some
mRNAs?
Answer:
These regions contain a core AUUUA and are used to destabilize mRNA and lead
to rapid degradation. Specific proteins can bind to these regions and recruit de-
adenylating enzymes and exosome (rapid 3' to 5' degradation). Because of this
recruitment function, AREs are usually found in short-lived mRNAs.
,Question:
4. Compare and contrast the two deadenylation dependent
mRNA decay pathways.
Answer:
The first pathway discussed involves the degradation of the mRNA in the 3' to 5'
direction using exosome. The second pathway discussed involves extra enzymes
that have to remove the 5' cap (DCP1 and 2) in order for a different enzyme to
degrade the mRNA in the 5' to 3' direction (XRN1).
Question:
5. What happens to an mRNA that utilizes the
endonuclease-mediated mRNA decay pathway?
Answer:
This pathway does not rely on the de-adenylation of the mRNA prior to
degradation. The mRNA can be cut in the center by endonuclease, which
provides an open 3' and 5' end. The exosome can come in a degrade the 5' end of
the mRNA in a 3' to 5' direction while XRN1 can degrade the 3' end in the 5' to 3'
direction.
Question:
6. What is XRN1?
Answer:
A 5' to 3' exonuclease
Question:
7. What is exosome?
Answer:
The main 3' to 5' exonuclease in the cell
Question:
8. What is deadenylation?
Answer:
The shortening (and ultimate removal) of poly(A) tail of mRNA
, Question:
9. What mRNA components are key to mRNA
circularization?
Answer:
PolyA tail, PABP, eIF4G, eIF4E, and the 5' cap
Question:
10. What is endonuclease?
Answer:
An enzyme which cleaves a polynucleotide chain by separating nucleotides other
than the two end ones
Question:
11. What is a synonymous codon?
Answer:
Codons that encode for the same amino acid
Question:
12. Why is the genetic code considered degenerate?
Answer:
Because of the presence of synonymous codons (amino acids can be coded for
by multiple codons)
Question:
13. What is the significance of the AUG codon?
Answer:
This is the "start" codon (methionine), which indicates where translation should
begin
Question:
14. Why are there codons that do not code of an amino
acid?
Answer:
Because these are the "stop" sites to indicate where translation should end (UAG,
UAA and UGA)
QUESTIONS AND CORRECT ANSWERS
Question:
1. Do all mRNA have the same steady state concentration?
Why or why not?
Answer:
No. The steady state concentration is dependent on the rate of synthesis and the
rate of degradation. For example, ribosomal proteins are always needed and
therefore have much more stable mRNAs so the proteins can be consistently
made. However, cytokines are condition dependent and are only needed under
certain conditions. Therefore, their mRNA is less stable because the proteins are
only needed conditionally.
Question:
2. Deadenylation of an mRNA results in the loss of the
polyA binding protein. What role does this play in
facilitating mRNA degradation?
Answer:
De-adenylation of mRNA by the deadenylase complex begins at the 3' end of the
poly-A tail and removes the A residues until the poly-A tail is removed. This results
in a loss of the PABP (normally bound to poly-A and eIF4G to prevent
degradation), which is a key protein to the circularization of the mRNA. When the
3' end is exposed, the exosome can come in and degrade the mRNA in the 3' to 5'
direction. Alternatively, after the poly-A tail is removed, the mRNA can be de-
capped (via DCP1/DCP2) then degraded from the 5' to 3' end using XRN1
(predominant pathway in yeast but not mammals).
Question:
3. What is the significance of the ARE (AU-rich elements)
found in the 3' non-translated region (NTR) of some
mRNAs?
Answer:
These regions contain a core AUUUA and are used to destabilize mRNA and lead
to rapid degradation. Specific proteins can bind to these regions and recruit de-
adenylating enzymes and exosome (rapid 3' to 5' degradation). Because of this
recruitment function, AREs are usually found in short-lived mRNAs.
,Question:
4. Compare and contrast the two deadenylation dependent
mRNA decay pathways.
Answer:
The first pathway discussed involves the degradation of the mRNA in the 3' to 5'
direction using exosome. The second pathway discussed involves extra enzymes
that have to remove the 5' cap (DCP1 and 2) in order for a different enzyme to
degrade the mRNA in the 5' to 3' direction (XRN1).
Question:
5. What happens to an mRNA that utilizes the
endonuclease-mediated mRNA decay pathway?
Answer:
This pathway does not rely on the de-adenylation of the mRNA prior to
degradation. The mRNA can be cut in the center by endonuclease, which
provides an open 3' and 5' end. The exosome can come in a degrade the 5' end of
the mRNA in a 3' to 5' direction while XRN1 can degrade the 3' end in the 5' to 3'
direction.
Question:
6. What is XRN1?
Answer:
A 5' to 3' exonuclease
Question:
7. What is exosome?
Answer:
The main 3' to 5' exonuclease in the cell
Question:
8. What is deadenylation?
Answer:
The shortening (and ultimate removal) of poly(A) tail of mRNA
, Question:
9. What mRNA components are key to mRNA
circularization?
Answer:
PolyA tail, PABP, eIF4G, eIF4E, and the 5' cap
Question:
10. What is endonuclease?
Answer:
An enzyme which cleaves a polynucleotide chain by separating nucleotides other
than the two end ones
Question:
11. What is a synonymous codon?
Answer:
Codons that encode for the same amino acid
Question:
12. Why is the genetic code considered degenerate?
Answer:
Because of the presence of synonymous codons (amino acids can be coded for
by multiple codons)
Question:
13. What is the significance of the AUG codon?
Answer:
This is the "start" codon (methionine), which indicates where translation should
begin
Question:
14. Why are there codons that do not code of an amino
acid?
Answer:
Because these are the "stop" sites to indicate where translation should end (UAG,
UAA and UGA)
