Translational Regulation

Question 1

Question: What role does the 5’ cap play in eukaryotic translation initiation?

Answer 1

Answer: In normal eukaryotic translation initiation, the 5’ cap plays a crucial role in docking the eukaryotic initiation complex to the mRNA. The complex then scans the mRNA for the start codon. (SOURCE: L28 2024.pdf)

Answer: The 5’ cap is like a docking station at the start of the mRNA that helps the machinery of the cell to start reading and translating the mRNA into a protein.

Question 2

Question: What happens if some viral/eukaryotic mRNAs lack a 5’ cap?

Answer 2

Answer: Some viral/eukaryotic mRNAs lack a 5’ cap. In these cases, an internal ribosome entry site (IRES) on the 5’ side of the start codon is used to initiate translation. (SOURCE: L28 2024.pdf)

Answer: An IRES is like a secondary docking station inside the mRNA that can start the translation process even if the main docking station (the 5’ cap) is missing.

Question 3

Question: How does an Internal Ribosome Entry Site (IRES) function in translation?

Answer 3

Answer: The IRES interacts with the 40S ribosome subunit or the initiation factor eIF4F to start translation, bypassing the need for the 5’ cap. (SOURCE: L28 2024.pdf)

Question 4

Question: What is one experimental application of the Internal Ribosome Entry Site (IRES)?

Answer 4

Answer: An experimental application of IRES allows for the co-expression of several genes under the control of the same promoter. This means multiple genes can be simultaneously transcribed and translated from a single mRNA molecule. (SOURCE: L28 2024.pdf)

In experiments, scientists can use IRES to get a single mRNA to produce multiple different proteins at the same time.
Scientists can add an IRES into an mRNA sequence on purpose in order to control the expression of multiple proteins from the same mRNA. This doesn’t necessarily make the process faster, but it does allow for simultaneous production of different proteins from a single mRNA, which can be very useful in certain experimental or therapeutic contexts.
–> more than one ribosome can work on the same mRNA molecule at the same time. This is a process known as “polyribosome formation” or “polysomes”. Once a ribosome has moved far enough along the mRNA after initiating translation, another ribosome can attach to the start of the mRNA and begin translating. This means that multiple copies of the same protein can be made from a single mRNA molecule at the same time, making protein synthesis more efficient.

Question 5

Question: What are the three types of mRNA degradation?

Answer 5

Answer: The three types of mRNA degradation are 1) Nonsense-mediated mRNA decay, 2) Non-stop mRNA decay, and 3) No-go mRNA decay. (SOURCE: L28 2024.pdf)

Nonsense-mediated decay (when there’s a stop signal too early), Non-stop decay (when there’s no stop signal), and No-go decay (when the translation process gets stuck).

Question 6

Question: What is the process of Nonsense-mediated mRNA decay?

Answer 6

Answer: Nonsense-mediated mRNA decay is a process that detects and destroys transcripts with a premature stop codon. It involves the marking of each excised intron site by an exon junction complex (EJC) during pre-mRNA splicing. If a premature stop codon is present, the ribosome is released early and some EJCs remain on the mRNA. These EJCs recruit proteins that cleave the 5’ cap, leading to mRNA degradation by RNases. (SOURCE: L28 2024.pdf)

Question 7

Question: How does Non-stop mRNA decay work?

Answer 7

Answer: Non-stop mRNA decay is a process that detects and destroys transcripts without a stop codon. Without a stop codon, translation proceeds through the 3’ poly(A) tail, where AAA encodes lysine. A stalled ribosome binds a protein that triggers ribosome dissociation and mRNA degradation by a 3’ to 5’ RNase. The defective polypeptide is then degraded by a protease that recognises the C-terminal poly(lysine) tag. (SOURCE: L28 2024.pdf)

Question 8

Question: What is RNA interference and how is it induced?

Answer 8

Answer: RNA interference is a process of mRNA degradation induced by double-stranded RNA (dsRNA). It’s a mechanism that regulates gene expression and defends against viral RNA. (SOURCE: L28 2024.pdf)

Answer: RNA interference is like a security guard that destroys mRNAs that match a specific pattern, which helps control which genes are turned on and defends against viruses.

Question 8

Question: What triggers No-go mRNA decay?

Answer 8

Answer: No-go mRNA decay is triggered when the ribosome stalls before the stop codon is reached, for example, due to rare codons or secondary structure. The stalled ribosome recruits factors that promote ribosome dissociation, mRNA cleavage, and mRNA degradation. (SOURCE: L28 2024.pdf)

Question 9

Question: Where does dsRNA come from?

Answer 9

Answer: double-stranded RNA/ dsRNA can come from two sources: exogenous (e.g., from viruses or experimentally introduced) and endogenous (generated from larger transcripts made by RNA polymerase II/III). (SOURCE: L28 2024.pdf)

Question 10

Question: How is exogenous dsRNA processed?

Answer 10

Answer: Exogenous dsRNA is cleaved by an RNase called Dicer into 21 nucleotide-long fragments. These single-stranded cleavage products, called small interfering RNA (siRNA), bind Argonaute proteins to form an RNA-induced silencing complex (RISC). RISC then binds to target mRNA, stopping translation and/or causing mRNA degradation. (SOURCE: L28 2024.pdf)

iRNAs are like guides that show the RNA interference machinery which mRNAs to destroy.

Question 11

Question: How are MicroRNAs (miRNAs) generated and what is their role?

Answer 11

Answer: MicroRNAs (miRNAs) are generated from larger transcripts made by RNA Polymerase II or RNA Polymerase III. These transcripts are cleaved to form 21 nucleotide-long dsRNA, which is further processed into single-stranded RNA (ssRNA). The ssRNA binds to Argonaute to form RISC, which binds to target mRNA and inhibits protein synthesis. (SOURCE: L28 2024.pdf)

Answer: MicroRNAs (miRNAs) are made from larger RNA molecules and work like siRNAs to guide the RNA interference machinery.

Question 12

Question: Why must cellular iron (Fe) levels be tightly controlled?

Answer 12

Answer: Iron is needed for the synthesis of many proteins, such as haemoglobin, and is a key part of making ATP. However, excess iron can damage proteins, lipids, and nucleic acids via free-radical reactions. Thus, it’s crucial to maintain a balance. (SOURCE: L28 2024.pdf)

Question 13

Question: What roles do Transferrin, Transferrin receptor, and Ferritin play in controlling cellular iron?

Answer 13

Answer: Transferrin carries iron in the blood.
The Transferrin receptor binds iron and Transferrin, enabling iron entry into cells. Ferritin stores iron in the liver and kidney. (SOURCE: L28 2024.pdf)

Question 14

Question: How are Ferritin and Transferrin receptor levels reciprocally related?

Answer 14

Answer: When iron levels are low, Transferrin receptor levels increase and Ferritin levels decrease. When iron levels are high, Transferrin receptor levels decrease and Ferritin levels increase. This regulation takes place during translation. (SOURCE: L28 2024.pdf)

Question 15

Question: How is Ferritin synthesis regulated?

Answer 15

Answer: Ferritin mRNA has a stem-loop called the iron response element (IRE) in the 5’ untranslated region which binds to the IRE binding protein. When iron levels are low, the IRE binding protein binds to Ferritin mRNA and blocks initiation of translation. When iron levels are high, the IRE binding protein binds iron and so cannot bind to Ferritin mRNA, leading to Ferritin mRNA being translated and Ferritin storing excess iron. (SOURCE: L28 2024.pdf)

Question 16

Question: How is Transferrin receptor synthesis regulated?

Answer 16

Answer: Transferrin receptor mRNA also has several IRE regions in the 3’ untranslated region that bind to the IRE binding protein. When iron levels are low, the IRE binding protein binds to Transferrin receptor mRNA and translation proceeds as normal. When iron levels are high, the IRE binding protein binds iron and detaches from the Transferrin receptor mRNA, leading to rapid mRNA degradation and no translation. (SOURCE: L28 2024.pdf)

Question 17

Question: How is Nonsense-mediated mRNA decay different from No-go mRNA decay?

Answer 17

Answer: Nonsense-mediated mRNA decay and No-go mRNA decay are two types of mRNA degradation, but they respond to different issues in the mRNA.
Nonsense-mediated mRNA decay happens when there’s a premature stop codon. This means the ribosome stops translating too early, and so the mRNA is flagged for destruction to prevent the production of a potentially harmful incomplete protein.

On the other hand, No-go mRNA decay happens when the ribosome gets stuck or stalls during translation, perhaps due to a problematic sequence or structure in the mRNA. To prevent this stalled complex from causing issues, the mRNA is again targeted for destruction.

In simple terms, you can think of it like this: Nonsense-mediated decay is like a race ending too early because someone put the finish line in the wrong place, while No-go decay is like a race being cancelled because a runner got stuck and couldn’t move forward. (SOURCE: L28 2024.pdf)

Question 18

Which of the following statements regarding iron-
mediated control of ferritin synthesis is TRUE?
A. Ferritin transcript levels are altered in response
to cellular iron
B. Ferritin synthesis increases when cellular iron
levels are low
C. Ferritin synthesis increases when the IRE binding
protein binds to ferritin IRE
D. Ferritin synthesis increases when the IRE binding
protein is bound to iron
E. I don’t know

Answer 18

D is correct, when IRE binding protein is bound to iron, Transferrin receptor mRNA, leading to rapid mRNA degradation and no translation and hence ferritin synthesis increases and stores the iron.

A is incorrect because, the control of ferritin levels in response to iron is not at the level of transcript production (i.e., transcription), but rather at the level of protein production (i.e., translation). The amount of ferritin mRNA in the cell does not change with iron levels. Instead, iron levels influence whether the existing ferritin mRNA is translated into protein or not.

So, while iron levels do influence ferritin synthesis, they do this by controlling the translation of existing ferritin mRNA, not by altering the levels of the mRNA itself. Therefore, option A is incorrect.