My Blog List

Monday, May 2, 2011

which came first riboswitches or ribozymes?

We have discussed RNA a lot in the lecture class.  There is much more to talk about regarding these versatile molecules.  For instance, some RNA molecules can act like enzymes.  Origin of life enthusiasts believe that this supports the notion that early life was RNA based....the RNA world hypothesis. 

But on the other hand, some RNA is regulated by many outside factors.  Some of these factors interact with a region on the mRNA called riboswitches, these are binding sites within mRNA for molecules which help control the production of the protein which results from that particular RNA.  These molecules are the "dependent" cousins of the more independent ribozymes.  It would be interesting to see if ribozymes are controlled by riboswitches or they are dependent on them.

1 Provide an example for how riboswitches work.  What is the advantage of having a switch within the mRNA which is used for the translation process? (i.e., why could not the switch be outside the sequence?).

2 Riboswiches show that mRNA sequences are used for more than just making a protein...the same sequence can bind to factors which control the sequence.  What is the significance of one molecule of RNA having multiple functions?

3 Can you envision a scenario for how roboswitches could have evolved?


  1. 1. When an antibiotic pyrithiamine enters the cell, it is metabolized into pyrithiamine pyrophosphate. Pyrithiamine pyrophosphate has been shown to bind and activate the TPP riboswitch, causing the cell to cease the synthesis and import of TPP. Because pyrithiamine pyrophosphate does not substitute for TPP as a coenzyme, the cell dies. (Wikipedia). Riboswitches being in the mRNA allows it to directly control gene expression and the production of proteins. If it was outside the sequence it probably couldn’t be as effective.
    2. Depending on the needs of the cell, the same RNA can do different functions. Diversification would probably make the cell more versatile and able to be more efficient. It could also act as a backup mechanism, if the original system failed.
    3. Riboswitches could have been the original regulatory devises, before proteins were used. As organisms became more complex, they needed more functions and different sections of the RNA adapted to fulfill these deficiencies.

  2. 1 Provide an example for how riboswitches work. What is the advantage of having a switch within the mRNA which is used for the translation process? (i.e., why could not the switch be outside the sequence?).

    they seem to work as a part of gene expression in prokaryotes/eukaryotes by translation and by the regulation of ribosomal proteins. this is for making correct function of this structure,the advantage is. It is first used to speed up the expression cycle from DNA to mRNA to protein. by Using a riboswitch we can transcribe before before we need to make a DNA into an mRNA,which then always it to readily be translated in a seconds time. In essence, we can manufacture protein without having to wait for transcription.

    2 Riboswiches show that mRNA sequences are used for more than just making a protein...the same sequence can bind to factors which control the sequence. What is the significance of one molecule of RNA having multiple functions?

    they also can control translation, also it regulates downstream mRNA and manages the expressions of proteins. By inserting a "switch" between the DNA and RNA system we can make a thorough inspection into a single mechanism of both systems and the a very precise-effect between their regulatory factors.

    3 Can you envision a scenario for how roboswitches could have evolved?

    they could have evolved from the coding regions of the protein genetic factors the are produced in the same area as the genes they control. not really sure i can think of anything else that is similar to them.

    search this with google it is really helpful
    "Team:NYMU-Taipei/Project/Speedy Switch -" Main Page - Web. 03 May 2011. .

  3. 1.) According to wikipedia, a riboswitch is composed of two parts: “an aptamer and an expression platform. The aptamer (oligonucleic acid or peptide molecule) directly binds to the small molecule and the expression platform undergoes structural changes in response to the changes in the aptamer.” One example of a riboswitch in bacteria called the Glycine riboswitch which binds to glycine amino acids. When glycine is in excess within the cell, the riboswitch binds to the glycine and thus promotes glycine destruction. The cool thing about this riboswitch is that it has two aptamer parts which makes it more efficient in binding to glycine. On the other hand, riboswitches also control translation. When the aptamer binds to the molecule, the expression platform changes structure to either switch on or off. Sometimes it turns off and thus stops translation but self-cleaving caused by ribozymes. Because of this cleavage, the ribosomal binding site is blocked and thus translation is prevented.

    I think that one advantage could be that if the proteins that were being translated were unfolded or defective, this switch located directly within the mRNA could be turned off so that the chaperone proteins could have time to compensate. I think that this might have to do with the UPR (Unfolded Protein Response) which would prevent an overwhelming amount of unfolded and defective proteins from being made. Also by having the riboswitch on the mRNA, it could better organize gene expression instead of a competitive activation of RNA polymerases. Also, by being inside of the sequence of the mRNA, it could directly prevent the mRNA from being expressed by blocking the binding site of the mRNA.

  4. 1) Because the riboswitches are incorporated directly into the mRNA, there are less steps for the mechanism to go through, so less problems can be encountered. For instance, the switch Sam is talking about, the Glycine riboswitch, destroys glycine. This happens in very few steps when compared to other mechanisms that destroy glycine. Riboswitches are also much more specific about the ligands that bind to them. This also leads to fewer mutations in the RNA and fewer problems with the mechanism. The whole process can be accomplished much quicker also because there are so few steps to go through.

    2) One RNA having multiple functions lets the cell conserve space and time. Cells already spend a lot of time on making RNA and ribsosomes. Many of the genes are also dedicated to synthesizing RNA. So if they had to make RNA to do one thing and more RNA to do another and more RNA to do another, it would get very difficult to manage all of those RNAs. Combining functionality into one RNA means less RNA for the cell to produce.

    3) the idea of molecules evolving doesn't make any since to me....for something to evolve, it has to adapt, for something to adapt, it has to be alive. Molecules aren't alive. So how could they ever evolve?

  5. 1 Riboswitches are mRNA structures which regulate gene expression. They do so by binding to ligands which in turn affect the riboswitch to conform to a certain structure which cause termination of translation. An advantage of having a switch for translation is that it can control when certain proteins are needed so as to not create too many of them nor too little.

    2 The significance of having such diversity with just one molecule shows the necessity of RNA and the versatility that a single molecule can have. With one molecule having multiple functions allows the cell to be less constricted and more efficient as it only has to make one molecule for many functions

    3 Not really. The complexity of creating a switch to control protein synthesis is beyond me. This seems to be another reducibly complex system.

  6. 1. Riboswitches are made up of two parts: the aptamer and the expression platform, as Sean said. The aptamer binds the molecule and causes the expression platform to structurally change. It is this change in the expression platform that regulates the activity of the RNA. One example is the Lysine riboswitch (or L-box) which binds lysine. The binding of lysine causes the mRNA to stop coding genes for lysine biosynthesis, catabolism, and transport.
    Having the riboswitch within the mRNA allows the riboswitch greater range of effects on the mRNA. Since riboswitches are within the sequence they can affect the splicing of pre-mRNA (which can produce different reading frames). A riboswitch within each mRNA also allows more specific control over the genes. It would be much more difficult to a signal molecule to bind to another protein and then for that protein to find the correct mRNA and then switch the gene on or off. Riboswitches are a very efficient way to control mRNA activity.
    2. As I discussed in number 1, riboswitches allow the cell to be much more efficient. No other enzymes or signal proteins are needed, the mRNA can “know” when to stop or begin coding a gene.
    3. I have no idea how riboswitches could have evolved. What are the chances that the molecule would bind to the exact mRNA that codes for genes that regulate the molecule without the information already being put into the mRNA to bind that specific molecule? And even if it did where did this new sequence for a riboswitch come from and how would it be passed on to offspring?

  7. 1: There are many types of riboswitches but here are a few examples:
    Glutamine riboswitches bind glutamine to regulate genes involved in glutamine and nitrogen metabolism.
    Glycine riboswitch binds glycine to regulate glycine metabolism genes, including the use of glycine as an energy source.
    Purine riboswitches binds purines to regulate purine metabolism and transport.
    From these examples, it seems like an mRNA that contains a riboswitch is directly involved in regulating its own activity, in response to the concentrations of its target molecule. The switch can’t be outside the sequence because then it can’t regulate it’s own activity.
    2: I wasn’t able to find any good information on this but the only logical reason I can think of as to why one molecule of RNA has multiple functions is so that more processes can be done in a smaller amount of time. The cell and RNA specifically already has so many functions, and if the RNA has multiple functions, then the cell can get things doen faster and therefore be more effective.
    3: I don’t believe that the creation of the world was done by organisms evolving so I don’t see how this is in any way logical. It doesn’t make any sense to me.

  8. 1. In a riboswitch, the aptamer section binds to a molecule, and the expression platform that codes for the gene changes its structure so the gene expression is altered. A possible advantage to this could be inhibition of gene expression after the RNA has been made; as it is too late to use many inhibition mechanisms after transcription and processing.
    2. The fact that RNA has multiple functions could be a problem for origin of life scientists who suggest that RNA came before DNA, because RNA is more complex than originally thought; and all these mechanisms must be present and working in the first cell.
    3. I guess a possible way riboswitches could have evolved (using an evolutionary model) would be if many of the same organisms had a segment of RNA that coded for a protein that resulted in death under certain environmental conditions. If that were the case, an organism with a riboswitch would be able to survive those conditions and reproduce.

  9. 1. Riboswitches work by alternating between two different RNA secondary structures. They bind small effector molecules, such as nutrients and cAMP. They normally work by changing the stem and loop structure of the mRNA transcript. The advantage of having the riboswitch within the mRNA during the translation process is that it can directly affect the mRNA and shut translation off at the source. Especially if there is something wrong with the protein or if there are just too many proteins which are unfolded at that time. It reminds me of the UPR(Unfolded Protein Response) but in this case the riboswitch is even more effective because it is within the mRNA during the translation process.

    2. The significance of one molecule of RNA multiple functions shows a serious problem for evolution. Most people believe RNA to be the more simple nucleic acid that evolved into DNA. If RNA has multiple functions besides the one that it is most famous for which is the making of a protein then it is definitely evidence for a creative Creator. It also is so amazing that the RNA can bind to factors of RNA that control the sequence, if I read the statement correctly. I think that just shows how complicated RNA is. I know even hearing about the complexity of RNA and learning about all the different types of RNA in lecture before the last test I was amazed at the complexity that could be found in this very small component of a small cell and the accuracy that must be found there or a innumerable amount of things could go wrong. It amazed me every time.

    3. I can't envision a scenario for how ribosiwtches evolved but I guess if I really had to fabricate a situation, I would say that ribozymes came into being and then they really needed another component or they would die and so in came this thing called the riboswitch and attached itself to the ribozyme and the small ribozyme survived and overcame natural selection since evolution is survival of the fittest. I'm not really sure whether that made any sense.

  10. 3.) Building off of what susan said, in terms of the natural selection the evolutionist mind, there could have been mutated RNA that just so happened to have a part of it that started to bind to different molecules. Because of this mutation (as we know that mutations cause good things to happen :p) this caused this mutated cell to have better gene expression and thus was able to be more “fit” and able to outlive and survive better than other cells. Thus as this cell reproduced, making more cells with this "mutated" RNA.

  11. 1 Provide an example for how riboswitches work. What is the advantage of having a switch within the mRNA which is used for the translation process? (i.e., why could not the switch be outside the sequence?).
    An example for how riboswitches work is in
    E. Coli, the thiamine riboswitch is controlled by the thiamine pyrophosphate, a vitamin. When the vitamin is abundant it binds to the riboswitch close to the 5' end of mRNA and trascription of mRNA is aborted. Now when the vitamin is absent this allows transcription and translation to give enzymes to make more thianine. I think the advantage of having these ribsowitches inside the mRNA serves as a sensor of concentrations of their corresponding ligands so they can either change shape or catalyze an enzymatic reaction in response.

    2 Riboswiches show that mRNA sequences are used for more than just making a protein...the same sequence can bind to factors which control the sequence. What is the significance of one molecule of RNA having multiple functions?
    The significant of one molecule having multiple functions is that it serves almost as the "mother" molecule being able to detect any mutation or disfunction of the mRNA as well as controlling whether the mRNA is used or not, such as in Ecoli. Another significance of having multiple function could mean multiple purposes for mRNA to be carried out, which means it serves a purpose in the production of these proteins.

    3 Can you envision a scenario for how roboswitches could have evolved?
    they could have evolved from the metabolic pathways that they are now so frequently involved in as binding sites to regulate these pathways for appropriate mRNA function.

  12. Riboswitches work by sensing small molecule concentrations. (A small molecule is a low molecular weight organic compound that is not a polymer). The riboswitch then binds directly to the small molecule. This binding triggers the part of the riboswitch that controls gene expression. The binding can either make the riboswitch turn off or turn on gene expression.

    An advantage to this system is that if the genes begin to be made improperly, the whole system can shut itself down without needing another entity outside itself to do the job. This system is another protection against gene mutation.

    The significance of one RNA molecule having multiple functions is that now the whole system is more efficient. Instead of needing a couple systems to accomplish one goal (correct gene expression), only one system is needed to produce the right genes in the correct amounts.

  13. 1. Riboswitches have an aptamer which binds to Amino Acids. An example of this is when a riboswitch binds to a specific sequence that is in excess. In this manner, cell’s limit the amount of excess proteins. They can block the ribosomal binding site, preventing translation of the protein that is in excess. Increased efficiency, and better organization are a few of the advantages to having a switch within the mRNA.

    2. One molecule of RNA preforming multiple functions is efficient. In this case, mRNA can make a protein and bind to the factors that control the sequence. This way the contributing factors are naturally drawn to the mRNA without additional factors.

    3. Riboswitches require too many parts for function. They aren’t irreducibly complex. Without this feature, an evolutionary origin is impossible.

  14. 1.) A riboswitch a mechanism on a RNA strand, and is comprised of two parts: an aptamer (usually a peptide) that can bind to a target molecule, and an expression platform that alters its structure when the riboswitch binds to its target molecule. The changes in the expression platform are what alter the expression of the gene coded on that strand of mRNA. Some functions of riboswitches affect the translation process, such as the formation rho-independent transcription termination loops. In this process, the riboswitch causes part of the mRNA to base pair with itself causing it to disassociate from the RNA polymerase. The riboswitch can also fold itself in such a way as to separate it from the ribosome, thus ending translation as well. An advantage to having this kind of system built into the mRNA sequence is that it can be self-regulating.

    2.) If just one RNA molecule can perform several different functions then it allows the cell to be more efficient and get more mileage out of making just that molecule. It also makes it difficult to argue that RNA arose before DNA since RNA is far more complex than DNA in evolutionary terms since it performs multiple functions.

    3.) The difficulty in envisioning how a riboswitch would have evolved is that in order for one to work, the RNA must have a riboswitch aptamer that has a corresponding target molecule. Aptamers are only found on RNA with riboswitches, and since molecules don’t float around with corresponding aptamers, I can’t see how one could bump into an RNA strand and turn into a riboswitch. The vast diversity of riboswitches and their target molecules and folding functions also makes evolving difficult.

  15. 1 Riboswitches take on gene control functions that have long been thought to be the work of protein factors. Some riboswitches are capable of sensory and regulatory feats that are competitive with their protein counterparts. The advantage of having a switch is that you can turn off and on the translation process.

    2 It is more efficient and takes up less space. The multiple functions also allow there to be more mRNA which leads to more proteins.

    3 Riboswitches could have evolved from having small amount of proteins binding to a severe increase in binding proteins. Also maybe ribozymes initially had nothing to do with riboswitches but do to certain needs the ribozymes needed the riboswitches.

  16. 1. Riboswitches are divided into two parts, an aptamer and an expression platform. The aptamer is what binds to the molecule and the expression platform is changed as a result. This platform is what regulates gene expression. Generally these small molecules cause the expression platform to turn off gene expression. A more specific example of how riboswitches work is this: A ribozyme is contained in the mRNA and it encodes for a specific enzyme. Once this enzyme binds to it, it cuts of the 5’ end of the mRNA, which inactivates it. A benefit to this could be, we do not encode for too many proteins, and gene expression is regulated as well. There is a way to turn it “off.” If the switch was outside the sequence, an entire group of mRNAs could be turned off, instead of just one. It provides specificity.
    2. One molecule performing multiple functions provides us with a working cell. If mRNA did not function in multiple ways, we would not have a correctly functioning cell. We need it doing all of these different things in order to survive. It also makes sense, because if we were to have a molecule for every different function the mRNA carried out, our cells would be much larger and we would not be able to survive.
    3. If there is an “RNA World” there had to be switches to turn the processes on an off. Once DNA “evolved” these switches could go extinct due to natural selection. But, riboswitches, a more complex form, evolved instead. RNA molecules are now able to more precisely recognize molecules and respond accordingly.

  17. 1. An example of riboswitch function is in the biosynthesis of Vitamin B12. Riboswitches, directly bound to ligands, restrict transcription of parts of the RNA by changing the RNA structure. The control system of where the synthesis of one protein begins and another begins is made easier by riboswtiches. If it were not for them, proteins may have to be separated by some other means or even beocme dysfunctional.

    2. A molecule with many functions is an advantage as it saves energy--it is more compact than several units with each one only performing one function. Also, it serves as a self-destruct system because it is not tied to other parts of the synthesis complex more than it needs to be (though in this instance the whole process would stop anyway).

    3. From an evolutionary perspective, riboswitches may have originated from defectively transcribed DNA gene that may have coded for another protein. It may have had the factors bind to it to prevent the synthesis of a defective protein and it may have resulted in the halting of transcription or translation, depending on what the factor was and when it was applied. The cell may have developed a control mechanism for this and used it to regulate synthesis.
    Unfortunately, this hypothesis may also require cells to have minds, which they don't.

    Also, with regards to evolution, I would think that riboswitches came first because ribozymes help facilitate a process while riboswitches effect the process.

  18. 1."In one method, a ribozyme within the riboswitch could cleave itself when the expression platform binds to the small target molecule. This causes the riboswitch to fold such that the ribosome-binding site is blocked for translation.

    A second method involves intrinsic termination. In this instance, the mRNA molecule – containing the riboswitch – has a stem-loop structure rich in cytosine-gua nine base pairs followed by a chain of uracil residues. RNA polymerase binds tightly to the stem-loop, causing transcription to stall. The interaction between DNA and mRNA is weakened at the uracil chain due to weak adenine-uracil bonds, causing the complex to dissociate. Within the cell, riboswitches are most often used to regulate genes that make amino acids."

    If the switch is in the mRNA, it means one less piece needed for translation, and thus could make the whole process more reliable by cutting out a middle man.

    2. Since the riboswitches have different functions, it would make it harder for it to evolve. If it did evolve, how would it start off with one function and end up with the multiple functions now? Also, since it does many things, it means that it does not require more than 1 machine/parts to do all of the jobs, saving space in the cell, since the cells are so small.

    3. Since riboswitches help control the production of proteins, an evolutionary hypothesis could be that the first cells were having a hard time making enough proteins, and they needed something to help speed up the process, and also act as quality control.

  19. 1 Provide an example for how riboswitches work. What is the advantage of having a switch within the mRNA which is used for the translation process? (i.e., why could not the switch be outside the sequence?).
    Riboswitches remind me of a treadmill. When it's turned on, it burns certain areas of fat on the body and breaks it up. The Glycine riboswitch, like Sean said, bonds to the Glycine and helps break it down.
    The treadmill when it is on can also help you build muscle. Riboswitches also help translation and the gene sequence. So from what I'm getting from other people's comments...It has to bind to the inside of the sequence because it's quicker and takes less steps? (not sure)
    2 Riboswiches show that mRNA sequences are used for more than just making a protein...the same sequence can bind to factors which control the sequence. What is the significance of one molecule of RNA having multiple functions?
    I like Eric Frendt's and Susan's comments on this one! The significance comes from the evolutionary theory. Scientists believe that RNA evolved from DNA because RNA is so much more simpler, so it just built up to eventually become DNA. If that was true, how could you explain this one RNA that is complex and has multiple functions? I believe God placed that one RNA there for a reason, to prove all the more that He exists, that He is the creator of all things, and to give Him the glory that He deserves.
    3 Can you envision a scenario for how roboswitches could have evolved?
    Riboswitches may have been made from a mutation in the RNA sequence then had been passed down to future offspring? Not sure..maybe kind of like how the flies in class grew legs out of it's nose because someone messed with the sequence of genes. I don't really know...interesting question!

  20. Riboswitches are made up of two parts: an ampter, which targets certain molecules, and an expression platform that alters in structure when the ampter binds to a molecule. The changes in the expression platform are what effects gene expression. To give an example, Flavin mononucleotide riboswitches direct gene expression of bacterial genes involved in the biosynthesis and transport of riboflavin.

    The fact that one RNA molecule has various functions shows the cells reliance on this molecule. Without these specific molecules, the cell would not be able to perform different functions, which does not really fit the evolutionary model.
    In order to envision the evolution of riboswitches, we will have to look at it from the evolutionary model. Now the way life supposedly evolves is through mutations so if there was a mutated strand of RNA that would bind to certain molecules, that would be a start. If the mutation didn't cause any serious problems, the bacteria with the mutated RNA could pass the mutation down.

  21. 1.In a riboswitch, the aptamer binds to a small molecule and brings it to the expression platform, where it changed the structure depending on the aptameter. One thing riboswitches do is that it binds to the ribosome binding site, which inhibits the translation. This must be in the process else it would not have any effect.
    2.A problem presented is that the RNA if complex cannot have evolved to perform multiple functions. For such a basic unit of life to show such complexity causes the logic behind evolution to be severely questioned.
    3.It would be very hard, as the RNA would have had to been in place first to survive, and as they can’t exist without the riboswitches, it makes no sense.

  22. 1. Example: the rpoH gene of E.Coli is involved in the heat shock response. In addaiton to other forms of regulatin, the mRNA contains a thermonsensor domain, which controls the amount of translation. At normal temperatures, the thermosensor has a stem-loop structure that prevents translation. When the heat increases, the stem-loop structure falls apart and translation can occur. The advantages are riboswitches are very specific to their sustrates, binding of the substrate to the nascent transcript is required for a short time, and there is no involvement of another gene product, which reduces the effect of mutation that will deregulate the mechanism.

  23. Riboswitches are structures that form in mRNA and regulate gene expression in bacteria. Unlike other known RNA regulatory structures, they are directly bound by small ligands. The mechanism by which gene expression is regulated involves the formation of alternative structures that, in the repressing conformation, cause premature termination of transcription or inhibition of translation initiation. Riboswitches regulate several metabolic pathways including the biosynthesis of vitamins (e.g. riboflavin, thiamin and cobalamin) and the metabolism of methionine, lysine and purines. Candidate riboswitches have also been observed in archaea and eukaryotes. The taxonomic diversity of genomes containing riboswitches and the diversity of molecular mechanisms of regulation, in addition to the fact that direct interaction of riboswitches with their effectors does not require additional factors, suggest that riboswitches represent one of the oldest regulatory systems.

    3 Can you envision a scenario for how roboswitches could have evolved? from the given information above it would be nearly impossible for them to evolve.

  24. Riboswtiches work by small metabolites binding to noncoded region of the mRNA. Once bound to the metabolite, the riboswitches undergo a change in their folded conformation that allows them to alter the expression of a gene involved in production of that metabolite. Riboswitches have appeared as one new promising target for antibacterial defence. Also riboswitches suppress gene expression by blocking either termination of transcription or initiation of translation, which reduces the effect of mutation.

  25. 1. Riboswitch-controlled formation of rho-independent transcription termination hairpins leads to premature transcription termination.
    • Riboswitch-mediated folding sequesters the ribosome-binding site, thereby inhibiting translation.
    • The riboswitch is a ribozyme that cleaves itself in the presence of sufficient concentrations of its metabolite.
    • Riboswitch alternate structures affect the splicing of the pre-mRNA.
    • A TPP riboswitch in Neurospora crassa (a fungus) controls alternative splicing to conditionally produce an Upstream Open Reading Frame (uORF), thereby affecting the expression of downstream genes[23]
    • A TPP riboswitch in plants modifies splicing and alternative 3'-end processing [24][25]
    • A riboswitch in Clostridium acetobutylicum regulates an adjacent gene that is not part of the same mRNA transcript. In this regulation, the riboswitch interferes with transcription of the gene. The mechanism is uncertain but may be caused by clashes between two RNA polymerase units as they simultaneously transcribe the same DNA.[26]
    • A riboswitch in Listeria monocytogenes regulates the expression of its downstream gene. However, riboswitch transcripts subsequently modulate the expression of a gene located elsewhere in the genome.[27] This trans regulation occurs via base-pairing to the mRNA of the distal gene.

    2. Why this RNA-mediated mechanism of gene regulation? The advantages of the system are: (i) riboswitches are very specific to their substrates, suggesting a stringent control8. For example, the riboswitch– ribozyme of glmS RNA is specifically activated by GlcN6P but not with related compounds GlcN (glucosamine) and Glc6P (glucose-6-phospahte; Figure 2); (ii) binding of the substrate to the nascent transcript is required for a short time. Once the transcript is terminated the ligand can be dislodged from the site and can be reused either for the same or for other purposes; and (iii) there is no involvement of another gene product, which reduces the effect of mutation that will deregulate the mechanism. This might be the reason why it took long time to identify this control system. In spite of these advantages, the lack of universality might be due to some limitations like: (i) the 5¢ UTR may not form tertiary structures for all different kinds of metabolites; and (ii) riboswitch-mediated translational regulation is limited to mono-cistronic m-RNA.

  26. 1)Riboswitches are coding regions on the mRNA that bind to metabolites that regulate gene expression. the riboswitches are essentialy aptamer sequences that bind to small effector molecules specifically. These domains turn off/on the protein translation process and thus regulate mRNA activity. one advantage I can think of why it is separate from the sequence itself is that if the sequence becomes corrupted, it would tell itself to keep making faulty proteins, but if they are separate it can provide a check and balance system.

    2)By letting RNA take on multiple tasks and abilities, it allows for multitasking molecules, providing more space and more time to produce other important sequences or proteins

  27. 2.) This allows for the cell to be more efficient if the mRNA can perform multiplexors withing a cell this allows the cell for some freedom to produce other essential proteins that carry out other functions without having to spend energy or time on a separate protien doing the job the mRNA already does.

    3.) A way that they could have evolve would have been from a need from the early cell to have a system that would turn certain translation processes of so that in case a protien was being produced without cease and it was causing harm to the cell the processing would need to be turned off. This early cell would probably instead of having riboswitches it would produce enzymes that would stop the production of all proteins at once or a select few.

  28. A riboswitch is part of a molecule of mRNA that directly binds to a target molecule. Also, in response to the target molecule's concentrations, the mRNA directly regulates its own activity. The term came from the process of it sensing metabolite concentrations in small molecules. A majority of the time, these occur in bacteria, although some have been found to occur in plants and some types of fungi. They are also theorized to occur in archaea.

  29. 1 Provide an example for how riboswitches work.  What is the advantage of having a switch within the mRNA which is used for the translation process? (i.e., why could not the switch be outside the sequence?).
    riboswitiches are mRNA structures that regulate the way in which genes are expressed. they have two parts, the aptamer and the expression platform. an example would be the Glycine riboswitch. It binds to glycine amino acids. it promotes the destruction of glycine by binding to its amino acids. this switch controls translation and it can make it start or stop translating.

    2 Riboswiches show that mRNA sequences are used for more than just making a protein...the same sequence can bind to factors which control the sequence.  What is the significance of one molecule of RNA having multiple functions?
    it is significant because it allows the efficiency of the cell. it also presents a problem for the evolutionists in a "chicken or egg came first" kind of way. The RNA is incredibly complex, and to go to DNA would be reducing, but evolution promotion the increase of complexity over time. whiccchhh doesn't work. it would contradict the foundations of evolution.

  30. I think the significance of one molecule of RNA having multiple functions shows that RNA is not simple at all. It is contradict with the saying of evolution of simple life form. I couldn't envision a scenario for how riboswitches could have evolved. How does the switches know when to turn on and turn off by itself and start doing it job without other complex singaling or interaction that work together to make it happen. I cannot see any simplicity in this.

  31. I was gonna say thanks for stopping by my blog, but I got overwhelmed by all these smart people, I feel stupid now..

  32. Hi,

    A great article indeed and a very detailed, realistic and superb analysis, of this issue, very nice write up.

    Cytotoxicity Assay Kit

    Mark Holland

  33. Good article thanks thanks !!Wish You Good continuation .....