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Explainer: what is RNA?

Our genetic material is encoded in DNA (deoxyribonucleic acid). DNA is famous. But you may also have also heard of RNA (ribonucleic acid). So, what is RNA, and what is it good for? Quite a lot really…

RNA is similar to DNA in lots of ways. But an extra oxygen atom makes all the difference. Image from shutterstock.com

Our genetic material is encoded in DNA (deoxyribonucleic acid). DNA is famous. But you may also have also heard of RNA (ribonucleic acid). So, what is RNA, and what is it good for?

Quite a lot really. In fact, it is possible that early life used RNA as its genetic material and also used folded RNAs as chemical tools to survive. This is called the RNA world hypothesis.

RNA is similar to DNA in lots of ways. It is a long chain of sugars linked together by phosphate groups. There is a cyclic base attached to each sugar and the bases can pair with matching partners to make a double helix.

This resembles DNA but the helix is a bit contorted and often RNAs are folded into complex structures stabilised by short helices interspersed with long single-stranded loops.

The really important difference is that RNA has an extra oxygen atom. This makes RNA less stable than DNA.

Ribose, on the left, has one extra oxygen atom compared to deoxyribose, right. Wikimedia Commons

You might think that being unstable is a bad thing, but there are advantages. Organisms that need to change rapidly tend to use RNA as their genetic material. Viruses, such as influenza and HIV, choose RNA rather than the more stable alternative of DNA so they can change and keep one step ahead of the immune system of their hosts.

Many factors contribute to the high mutation rates in RNA viruses, including the instability of RNA and the poor proof reading activity in the enzymes that replicate RNA.

Messenger service

Like DNA, RNA is a long chain of sugars. Sponk

As well as serving as genetic material, RNA has another critical function in virtually all organisms: it acts as a messenger; a short-lived intermediate communicating the information contained in our genes to the rest of the cell.

Many genes need to be turned on in bursts. Think of a football fan shouting out at a key point in a game - we don’t want the message to last forever.

Genes do last a lifetime, so how do we provide short-lived messages?

We make RNA copies of our DNA genes. The messages, or mRNAs, reflect the sequence of bases in our DNA and travel out of the nucleus (where our DNA is stored) into the cytoplasm where they are translated into proteins. The proteins go on to do jobs in the cell and the unstable mRNAs simply decay or are degraded.

So RNA can act as a messenger in the process of ensuring genes are translated into proteins – the tools of the cell, things such as haemoglobin to carry oxygen round the body.

But how does this mysterious translation occur? Does it rely on chemical tools such as proteins?

It certainly does, but it seems that the proteins are not the key players. It is a remarkable fact that the really important players in triggering the chemical reactions to produce protein chains from the mRNA code are not other proteins, but specially folded RNA molecules - RNA enzymes or ribozymes.

The machinery for reading a protein from a messenger RNA is contained in a complex RNA enzyme and the functional parts are RNA molecules called ribosomal RNAs or rRNAs.

RNA enzymes or ribozymes trigger the mRNA translation process.

Securing information

How come RNA can trigger chemical reactions but DNA doesn’t seem to? It is partly the extra oxygen and partly the special ability RNA has to fold up into complex shapes to form tools that can do things, whereas the double helix is regular and stable. The DNA double helix holds information securely but doesn’t do much else.

In 1989 Sidney Altman and Thomas Cech shared the Nobel Prize in Chemistry for demonstrating that RNAs could catalyze chemical reactions.

You might wonder how a chain of sugars and bases such as mRNA can even serve as a template for forming a protein chain. The answer is complicated but it involves some clever adaptors. Amazingly, those adaptors are also made of RNA, they’re called transfer RNAs or tRNAs. They use their cyclic bases to pair to their mirror images in the mRNA and line up the right amino acids to make the protein, while the rRNA triggers the reaction to do the joining.

Structure of a transfer RNA (tRNA) molecule Image from shutterstock.com

The finding that absolutely essential functions such as encoding information, having a short-lived messenger to express it, and converting it into a set of functional protein tools, all involve RNA has led people to hypothesise that early life was made up of RNA.

In the beginning RNA possibly did the lot. But then gradually DNA took over as a more stable genetic material and proteins took over as more stable chemical tools. And RNA was gradually forgotten by some researchers, at least until recently.

Future of RNA

In 1998, American biologists Andy Fire and Craig Mello discovered RNA inhibition – how RNA can switch off genes.

We now know that a new class of small inhibitory RNAs (siRNAs which are about 20 residues long), fine tune the output from messenger RNAs. As mentioned RNA can form double strands - this allows siRNAs to bind messenger RNAs and interfere with their function.

These interfering RNAs are essentially “digital” inhibitors that are base for base mirror images of the messenger RNA. So it possible to make artificial inhibitors now. Thus a new industry has been born as researchers strive to turn genes off for experimental purposes and medical researchers investigate whether this can be used for therapies, such as turning off viruses or other harmful genes.

There has also been another interesting discovery – researchers have found that although only a small part of our genome encodes protein, around 2%, a much larger proportion is still copied into RNA.

The function of many of these long non-protein coding RNAs, called lncRNAs, is still being investigated but it seems that some act to catalyse chemical reactions and that others are involved in turning genes on or off either by binding messenger RNAs or by binding directly to the DNA genes they match.

If the world began with RNA then it is not really surprising that echoes of that RNA world remain and that RNAs are still involved in key life processes and are fundamentally important in gene regulation.

New classes of RNA molecules will continue to be discovered and it is seems likely that further insights into fundamental biology will emerge from this fertile ground in the future.

Join the conversation

30 Comments sorted by

  1. Dale Bloom

    Analyst

    RNA posses more questions.

    RNA is “a long chain of sugars linked together by phosphate groups”

    But sugars (or carbohydrates) are mostly formed by plants, and sugars don’t simply form in the atmosphere or form in minerals or dirt.

    So plants had to exist to make RNA, but before RNA existed, plants could not exist.

    So what existed before RNA?

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    1. Peter Campbell

      Scientist (researcherid B-7232-2008)

      In reply to Dale Bloom

      Predictable creationist nonsense.
      Sugars are made and used by all known forms of life.

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    2. Dale Bloom

      Analyst

      In reply to Peter Campbell

      Carbohydrates are originally derived from photosynthesis, and plants start all food chains.

      So how did plants exist and carry out photosynthesis before RNA or DNA?

      One of the criteria that defines a living thing is that it can reproduce and grow, so how did any living thing reproduce and grow before RNA or DNA?

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    3. Mike Swinbourne

      logged in via Facebook

      In reply to Dale Bloom

      "....So how did plants exist and carry out photosynthesis before RNA or DNA?..."

      Ever heard of cyanobacteria?

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    4. Dale Bloom

      Analyst

      In reply to Mike Swinbourne

      Cyanobacteria carry out photosynthesis.

      Products from photosynthesis include glucose molecules, and life forms can store glucose molecules in various forms as a way of storing energy.

      Herbivores and omnivores obtain their carbohydrates by eating plants (which carry out photosynthesis), and carnivores obtain their carbohydrates by eating herbivores and omnivores.

      Plants are the original source of carbohydrates.

      But the genotype of cyanobacteria is to carry out photosynthesis, and the cyanobacteria must have had genetic material to carry out reproduction.

      RNA and DNA require carbohydrates, so how did life forms exist before they were able to carry out the extremely complex process of producing carbohydrates, and then were able to include carbohydrates into the complex arrangement of RNA and DNA.

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    5. Peter Campbell

      Scientist (researcherid B-7232-2008)

      In reply to Dale Bloom

      And before cyanobacteria, and still today, non-photosynthetic bacteria make sugars and use them for all sorts of biochemistry, not just energy storage, not just making nucleic acids. If a human is starving we make sugars from certain amino acids.
      Sugars are part of the most fundamental biochemistry that predates photosynthesis and still occurs in its absence. Biology makes no sense except in the light of evolution. On the other hand you can commit intellectual suicide and just resort to 'god did it' everytime you don't know.

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    6. Dale Bloom

      Analyst

      In reply to Peter Campbell

      I haven't mentioned a God, but if as you say bacteria can make sugars, then how did they know how to do that without DNA or RNA.

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    7. Stuart Purvis-Smith

      Clinical Cytogeneticist (retired)

      In reply to Dale Bloom

      Dale, to assist your thinking in relation to the chicken and egg issues which have been raised in your recent posts: it is just possible that sugars can be formed in a prebiotic environment without pre-existing bacteria, RNA or DNA. The following link suggests as much with the title " Prebiotic synthesis of simple sugars by photoredox systems chemistry".
      http://www.nature.com/nchem/journal/v4/n11/full/nchem.1467.html

      The physicist, Professor Brian Cox in an excellent documentary of the ABC last night said of the origin of life on earth "...far from being some chance event ignited by a mystical spark, the emergence of life on earth may have been the inevitable consequence of the laws of physics".

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    8. Dale Bloom

      Analyst

      In reply to Stuart Purvis-Smith

      There may have been some ultraviolet irradiation, but I didn’t think there was that much hydrogen cyanide and cyanometallates around, and rather toxic to living things I would presume.

      It is also a rather huge step to take some carbohydrates and then transform them into RNA and DNA.

      I do think bacteria were involved in the creation of Earth’s early atmosphere, but the concept that bacteria developed on Earth by accident is implausible.

      More plausible that they were purposely put here.

      "If we want to colonize a planet, and have some kind of microbial system to produce food and oxygen, we’d have to design organisms best-suited for those conditions," he said. "Our ability to design organisms is already here. And as we get more and more genome sequences, and better understand the genes involved, we can construct a bug that not only can photosynthesize and make oxygen, but live under conditions not found on Earth."
      http://www.wired.com/wiredscience/2008/07/extraterrestria/

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    9. Mike Swinbourne

      logged in via Facebook

      In reply to Dale Bloom

      "....but the concept that bacteria developed on Earth by accident is implausible...."

      And yet, here they are.

      "....More plausible that they were purposely put here...."

      And where did they come from any how did they develop there?

      That's the problem with your position Dale. Life exists. And since it exists, it must have developed at some time or other. If you want to go down the track and argue that life was put on Earth in the past, then you are going to have to provide some sort of explanation for its development elsewhere.

      And if you are then going to argue that 'god did it', then please tell us where god came from. And no - saying that god always existed is not an answer. If you are going to argue that life must have been created, then your god must have also been crerated as well. Its much easier to simplify the process and simply rely on the laws of physics and chemistry, because, after all, that's all that life is.

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    10. Peter Campbell

      Scientist (researcherid B-7232-2008)

      In reply to Dale Bloom

      So, hydrogen cyanide is a well known toxin so it can not have had a role in prebiotic development of building block compounds and early life?
      Let's examine that. What makes HCN a toxin? Answer: It binds tightly in the active site of the last enzyme in a set of enzymes that catalyses a biochemical pathway that taken together is called 'respiration'. That prevents the step in which oxygen is 'reduced' to water using reducing equivalents that have been passed along an 'electron transport chain'. Rather than writing out an undergraduate biochemistry lecture, suffice it to say that cyanide is toxic to organisms that respire with oxygen, an adaptation coming after the planet was flooded with oxygen by photosysthesising organisms long after the origins of life.

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    11. Dale Bloom

      Analyst

      In reply to Peter Campbell

      I think the argument is getting thinner. So organisms were able to develop something similar to amino acids and then develop RNA by metabolising compounds containing cyanide, but after they developed cellular respiration, cyanide compounds became toxic to them.

      I don’t know how they survived that change over period, because it is either one or the other.

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    12. Dale Bloom

      Analyst

      In reply to Mike Swinbourne

      There are currently organisations such as NASA’s Astrobiology Department that employ people such as John Baroos, who researches how to put life on other planets

      http://livingintheuniverse.com/Interviews/baross.html

      I think it a little elitist and pretentious if we were to consider ourselves the only possible life forms in the universe that could do that.

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    13. Mike Swinbourne

      logged in via Facebook

      In reply to Dale Bloom

      Dale

      No-one is denying that we are the only life forms in the universe, and while we don't yet have the capability to place lifefoms on other planets, its probably a safe bet that, if we survive, we will be able to do so at some point in the future.

      But that isn't what we are discussing here. The issue is where did the original RNA, carbohydrates and photosynthesis etc come from on Earth? And yes, it is a reasonable position to take that it may have come from somewhere else (transpermia…

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    14. Mike Swinbourne

      logged in via Facebook

      In reply to Mike Swinbourne

      Oops, finger trouble - I meant to say that 'no-one is suggesting that we are the only life forms in the universe'.

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    15. Dale Bloom

      Analyst

      In reply to Mike Swinbourne

      There are only three possible scenarios.

      1/ Life formed on the planet, and then life eventually developed RNA and DNA.
      2/ Life found its way onto the planet from elsewhere.
      3/ Life was purposely put onto the planet.

      There have been a lot of hypotheses regards how life could form on Earth, but not one hypotheses has been proven yet, which leaves 2 and 3.

      The matter probably has minimal relevance to someone who’s greatest concern is how to pay the monthly mortgage or electricity bills, and where life started may never be known anyway.

      But RNA and DNA do become relevant if we want to carry out terraforming of another planet or moon.

      http://www.lpl.arizona.edu/~jmoores/Terraforming.pdf

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    16. Peter Campbell

      Scientist (researcherid B-7232-2008)

      In reply to Dale Bloom

      It seems clear that you wish to make an argument from incredulity in favour of a creationist view.
      Not all forms of life use oxygen for respiration today. The chemistry of the planet has changed dramatically over geological time. A compound that is abundant at one time can be rare at another etc. I suggest you read some biochemistry and geology.

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    17. Peter Campbell

      Scientist (researcherid B-7232-2008)

      In reply to Dale Bloom

      Another non sequitur. It would be just as reasonable to argue that neither hypothesis 2 or 3 has been proven, which leaves only 1.
      Frankly, I think you like 3 but are being coy.

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    18. Dale Bloom

      Analyst

      In reply to Peter Campbell

      I am not being coy about it.

      No evidence has been found that life forms suddenly developed on this planet out of some primeval soup of chemicals (and it remains as hypothesis only).

      As well, the idea that life on this planet is the only life in the universe is rather like believing the Sun orbits the Earth.

      However, whether or not life forms did develop on this planet is all rather academic, and the real question now is whether or not we should attempt to put life forms on other planets or moons.

      By some people’s estimations, we currently have the technology to do that.

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    19. Peter Campbell

      Scientist (researcherid B-7232-2008)

      In reply to Dale Bloom

      "No evidence has been found ... remains as hypothesis only..."
      While it is a hypothesis, it is the hypothesis with the greatest level of support from diverse lines of evidence.
      It is fact that RNA can both encode information and catalyse reactions. It is a fact that it is a polymer of much simpler compounds. It is also fact that many of the most universal and fundamental aspects of biochemistry are performed by RNA such as the key steps in protein synthesis, according to the information in RNA…

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    20. Mike Swinbourne

      logged in via Facebook

      In reply to Dale Bloom

      "....No evidence has been found that life forms suddenly developed on this planet out of some primeval soup of chemicals (and it remains as hypothesis only)...."

      Actually Dale, there is very strong evidence that life forms developed on this planet - you, me, and all the other life forms on the planet. That's pretty compelling evidence right there. Does it prove it? No. But it remains compelling evidence.

      Because there are only two possible alternatives. It started here, or it came here…

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    21. Dale Bloom

      Analyst

      In reply to Peter Campbell

      You seem to be inferring that life started with RNA, and RNA formed out of a mixture of chemicals (and some type of energy source).

      But RNA and DNA has to be protected or enclosed to ensure it does not become contaminated or simply destroyed by other chemicals.

      Cells protect RNA and DNA, and in fact, the cell could be thought of as something that carries and protects RNA and DNA, and enables RNA and DNA to exist.

      So the formation of RNA and DNA is not enough, and for RNA and DNA to exist, cells also had to form at exactly the same time.

      Cells have a very sophisticated operation, and it becomes even more implausible that RNA or DNA and cells could all form at exactly the same time out of a mixture of chemicals.

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    22. Stuart Purvis-Smith

      Clinical Cytogeneticist (retired)

      In reply to Dale Bloom

      Dale, please do not take offence but if you come into a conversation about science armed with half-baked science, the sword of faith and the shield of ignorance, you can't really expect to be taken seriously.

      Let me ask you (and I would like a direct answer) - did you read the whole of the interview with Astrobiologist/ Oceanographer John Baross which you posted in support of your argument for the "seeding" of life on earth and beyond? He is on the same page as Peter and Mike in this thread and ends with the following:
      "I think there’s something inevitable about creating some kind of carbon-based life, based on the physics of how elements come together and how reactions occur on various metallic minerals".You might also be interested in a related item:
      http://www.lostcity.washington.edu/story/About where you will find essentially the same ideas.

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    23. Dale Bloom

      Analyst

      In reply to Stuart Purvis-Smith

      I read the John Baross interview, and noted the various hypotheses, and also noted the lack of tangible evidence that any hypotheses has actually occurred in reality.

      So that is why there are now so many hypotheses, (and a new one seems to come out ever year), because none have ever been proven.

      Also noted that he wants to put microbes onto other planets as a means of terraforming, but he starts with a living cell, where life has already formed.

      I am wondering if he has ever thought the same once occurred on planet Earth.

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    24. Peter Campbell

      Scientist (researcherid B-7232-2008)

      In reply to Dale Bloom

      "But RNA and DNA has to be protected or enclosed to ensure it does not become contaminated or simply destroyed by other chemicals."
      And many sources of such a function have been suggested. From memory these include binding and concentration on the surface of clay particles that have book leaf-like stacks, porous mineral structures around hot springs and vents, micelles of detergent-like compounds, fluid inclusions trapped in precipitated salts...
      BTW, another idea that is appealing is that many…

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    25. Stuart Purvis-Smith

      Clinical Cytogeneticist (retired)

      In reply to Dale Bloom

      I have a strong sense of deja vu ....again. The conversation is becoming rather pointless isn't it? But I take you back to to your 3 scenarios Dale:
      "1/ Life formed on the planet, and then life eventually developed RNA and DNA." - In my book that involves evolution from early life precursors to more complex life but in another conversation you have said:
      "The theory of evolution is a theory to pacify the masses .."
      So I guess that rules out scenario 1 unless you are proposing that all life…

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    26. Dale Bloom

      Analyst

      In reply to Stuart Purvis-Smith

      Lets just say you want to believe that life spontaneously formed one day on planet Earth, (just for something to do), but I keep an open mind as to the origins of life on planet Earth.

      The bigger question is whether or not we spread RNA or DNA onto other planets.

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    27. Stuart Purvis-Smith

      Clinical Cytogeneticist (retired)

      In reply to Dale Bloom

      "Lets just say you want to believe that life spontaneously formed one day on planet Earth....". No Dale, I am sorry if you misunderstood me but I guess that irony was wasted in this discussion. I am open to any scenario for the emergence of life on this planet or elsewhere as long as it is supported by scientific evidence and is consistent with the fundamentals of physics and chemistry as we currently understand them. The scenario to which I am not open is that of some kind of "creator" seeding life across the universe at will.
      Maybe I am a little slow so let me ask a final question of you: Why do you say that "The bigger question is whether or not we spread RNA or DNA onto other planets"? How is this important to you and how is it relevant? Why does it have to be RNA or DNA rather than some other simple self replicating molecule?

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    28. Dale Bloom

      Analyst

      In reply to Stuart Purvis-Smith

      At present it would seem that RNA or DNA are best at holding genetic information and creating a living thing.

      As opposed to say holding information in a computer chip onboard a robot.

      Although it could be said that living thing exists so that their RNA or DNA can be carried forward to the next generation, as no life form can live forever.

      But regardless of that, self replicating is not enough, as the organism has to live long enough to replicate.

      It all becomes rather involved, but if there is a moon or planet in a habitable zone of a solar system (and there could be 60 billion of such in our Milky Way galaxy), then would we leave that planet or moon empty of life.

      Or would we fill the planet or moon with self-replicating but non-living mechanical and electrical robots.

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