Riboswitches - Online Tutor, Practice Problems & Exam Prep

Riboswitches

Hi. In this video, we're going to be talking about riboswitches. So I kind of think riboswitches are kind of the coolest things ever, but I don't know. Maybe after this video you'll agree with me. So what are riboswitches? Riboswitches are mRNA sequences found in the 5' prime region, which stands for the region that obviously is not translated into protein, but it's still present in the mRNA. And so it's the sequence in the 5' prime untranslated region, and it binds small molecules, just molecules in general, and this controls gene expression of the mRNA itself. And so, riboswitches control the expression of themselves. It controls the expression of that mRNA sequence where the riboswitch exists. And so there are 2 main domains in a riboswitch. There is an aptamer, and this is the RNA sequence. Remember, when we were dealing with RNA, is an RNA sequence that binds to the small molecule, and then you have an expression platform. So after that is bound, a secondary structure forms and this regulates gene expression, and the secondary structure forms in this expression platform. So a common structure that will form is called the terminator structure. Now, all of these I feel like everything in this chapter is called the same thing, but it means different depending on which operon or what you're talking about, but for a riboswitch, the terminator structure, is a structure formed by binding the small ligand, and it terminates the translation. So riboswitches actually have the ability to interfere with transcription. It has the ability to interfere with splicing and translation. Now, it can interfere with transcription because remember, we're talking about prokaryotic cells, in these topics, and prokaryotic cells transcription and translation occur in the same compartment. And so riboswitches, even though they're happening on mRNA, can actually in the 5' prime regional region, it can affect transcription and translation. So when it stops transcription, ribos, so transcription termination, so the termination of transcription is controlled through that terminator structure, which I talked about before, and translation termination is controlled through a termination structure, so the same structure, but this one actually will block a ribosome binding site. So it can affect both transcription and translation depending on when and where all these structures are found. So this is what they look like. I think they have a really cool structure. One of the questions I hope that you're asking right now is you're saying, okay, well this is RNA, What are all these letters standing for? Why are there w's, k's, d's, y's, etcetera? Well, you'll notice here, any of the red ones, I believe, red and then some of these orange ones, these are actually nucleotides. And all of these stand for RNA nucleotides, but they stand for different things. Now I don't know the key off the top of my head, but we could say, well, W would stand for A or U, K would stand for T, G, or U. And all of these are different codes, and they stand for different combinations of what nucleotide could be there. But all of these little circles represent some type of nucleotide, even if it's not saying which nucleotide it represents and instead is in a code. So hopefully you asked that question. Notice here that this is 5' prime and 3' prime, so it goes down like this, creates these structures, goes all the way back around, and ends up here. So we're going that way, right, all the way around. So riboswitches are so cool. Hopefully, you think so too, but this is definitely a type of prokaryotic gene regulation, which can stop transcription or translation. So, with that, let's now move on.

Riboswitches are made up of what type of molecule?

• A. RNA
• B. DNA
• C. Protein

Which of the following processes can riboswitches NOT interfere with?

• A. Enhancers
• B. Transcription
• C. Splicing
• D. Translation

Here’s what students ask on this topic:

What are riboswitches and how do they function in gene regulation?

Riboswitches are mRNA sequences located in the 5' untranslated region (UTR) that bind small molecules to regulate their own gene expression. They consist of two main domains: an aptamer, which binds the ligand, and an expression platform that forms a secondary structure, often a terminator structure, to control transcription and translation. When the aptamer binds to a specific ligand, it induces a conformational change in the expression platform, leading to the formation of a secondary structure. This structure can either terminate transcription by forming a terminator structure or block the ribosome binding site, thus inhibiting translation. This mechanism allows riboswitches to effectively interfere with both transcription and translation in prokaryotic cells, playing a crucial role in gene regulation.

What are the main domains of a riboswitch and their roles?

A riboswitch consists of two main domains: the aptamer and the expression platform. The aptamer is an RNA sequence that binds to a specific small molecule or ligand. Upon ligand binding, the aptamer undergoes a conformational change. The expression platform is the region that forms a secondary structure in response to the aptamer's conformational change. This secondary structure can regulate gene expression by either terminating transcription through the formation of a terminator structure or blocking the ribosome binding site to inhibit translation. Together, these domains enable the riboswitch to control gene expression in response to the presence of specific ligands.

How do riboswitches affect transcription and translation in prokaryotic cells?

Riboswitches can affect both transcription and translation in prokaryotic cells. During transcription, the binding of a ligand to the aptamer domain can induce the formation of a terminator structure in the expression platform, leading to premature termination of transcription. In translation, the secondary structure formed in the expression platform can block the ribosome binding site, preventing the ribosome from initiating translation. Since transcription and translation occur in the same compartment in prokaryotic cells, riboswitches can simultaneously influence both processes, providing a versatile mechanism for gene regulation.

What is the terminator structure in a riboswitch and how does it function?

The terminator structure in a riboswitch is a secondary structure formed in the expression platform upon ligand binding to the aptamer domain. This structure functions by causing premature termination of transcription. When the terminator structure forms, it creates a hairpin loop followed by a series of uracil residues, which destabilizes the RNA-DNA hybrid in the transcription complex, leading to the release of the RNA polymerase and termination of transcription. This mechanism allows the riboswitch to regulate gene expression by controlling the length of the mRNA transcript.

What types of molecules can riboswitches bind to regulate gene expression?

Riboswitches can bind a variety of small molecules to regulate gene expression. These molecules include metabolites, such as vitamins (e.g., thiamine pyrophosphate), amino acids (e.g., lysine), nucleotides (e.g., guanine), and metal ions (e.g., magnesium). The specific binding of these ligands to the aptamer domain of the riboswitch induces a conformational change that affects the expression platform, leading to the regulation of transcription or translation. The diversity of ligands that riboswitches can bind allows them to play a crucial role in responding to various cellular and environmental signals.