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Science

New Amino Acid Discovered 142

Posted by timothy from the lookie-here-fellas-it's-another-one dept.
EricMargel writes: "As published in Science, researchers at the Ohio State University claim to have discovered the 22nd known amino acid, pyrrolysine, the first discovered since 1986." I hope rice and beans are still sufficient to get all the needed amino acids.
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New Amino Acid Discovered More

New Amino Acid Discovered

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  • Time for suppliment companies to make a quick buck on a new protien

  • Re: (Score:1, Offtopic)

    by account_deleted ( 4530225 )
    Comment removed based on user account deletion

    • Re:These scientists need to work on... (Score:4, Interesting)

      by BadDoggie ( 145310 ) on Sunday May 26, 2002 @07:52AM (#3586742) Homepage Journal
      Umm.. hello?

      Beano is the magic pill. Alpha-galactose. True, it's an enzyme, not a protein, but a protein isn't going to stop farts, which are mainly caused by sugars we can't digest but which the bugs in our intestines can.

      woof.

      • Enzymes are proteins that act as catalysts. So it is a protein.
      • So is that alpha-galctose an enzyme that will break down carbohydrates while the stomach environment is acidic? Thus removing the problem of the natural enzymes not being able to break down carbs in an acid environment? Or is something else happening?

        I wonder if it's really healthy... I like beans :) but I don't eat them because they aren't very good for your body.
        • The stomach is acidic, but if you've ever taken a shit and seen corn, or penuts, you'd know that acid doesn't break down everything (and, your stomach will get overwhlmed with food when you eat).

          In the small intestine are billions of bacteria that help your digestion process. In fact 50% of your poop isn't food, it's dead bacteria!

          If you don't have an enzyme to break the sugar down and absorb it, bacteria in the (usually large) intestine will. They break down the lactose, galactose, etc, and produce ... methane (ie - farts).

          If you take your beano or lactaid, it provides an enzyme that will break down the sugar into simpler components that you can absorb, so the bacteria won't process them.

          Most pills you take are 90+% buffer. Stomach acid will dissolve the outer part, and leave anything inside untouched.

      • Processed foods, powdered sugars, flour, etc
    • A better way to prevent gas is to learn how to combine foods properly. And to avoid bad foods like beans and dried lentils.

      Beans alone break the first rule of food combining; Don't eat carbs and proteins together.

      To break down protein which is an acid your stomach has to create an acidic environment. Carbohydrates are alkaline. The enzymes that break down Carbohydrates require an alkaline environment and can not function in the high pH environment required for proteins. So after being continuously bathed in acid and not allowed to digest, the carbs will finally move on to your small intestines where the environment is alkaline again and then, finally, start digesting.

      Food goes bad inside your body just like it does on the table. And your body temperature is a lot higher than room temperature, which seems to accelerate the process. You've heard of carbohydrates "fermenting" inside of you right, and that's why you get gas after eating beans? I think the word "rot" is a little less misleading.

      Other than itroducing rotting food into your body, beans also make your stomach produce a very acidic environment, which is bad for your overall health.

      Point is, beans are bad foods. Unless you just don't have a choice, you are better off eating something else. But if you are buying beano and so on, I'd assume you have another choice.
      • Beans alone break the first rule of food combining; Don't eat carbs and proteins together.

        I'm familiar with the "rules of food combining" ideas, though I don't really think it works. But in any case, you're misinterpreting it. Let me quote directly from A Complete Guide to Nature Cure [healthlibrary.com]'s chapter on food combining [healthlibrary.com]:

        "The most important rule for combining foods is to avoid mixing protein and carbohydrate concentrated foods. Although every food contains some protein , those regarded as protein concentrated foods demand the longest digestive time."

        By these rules, what you are avoiding is meals where you are eating both protein concentrated and carbohydrate concentrated foods. Key word is "concentrated." Beans aren't protein concentrated. They have high carbs and are low in protein. They don't "rot" inside your body. They are in general a great source of carbs and very good for you.

        It sounds to me like you read a lot of questionable information and took it as truth. Don't believe everything you read. Give beans a try again, they really are good foods.

        I never have gas because of any kind of beans, even refried beans. I usually eat raw vegatables (spinach, carrots, lettuce, etc) with my meals which seems to help digestion. Just out of curiosity, what is your diet like?

        BTW That nature cure book I linked to has a chapter on amino acids [healthlibrary.com].
        • Those manuals use the word concentrated generously. In that context it can also mean cooked or processed.

          Also, dried beans are concentrated proteins and concentrated carbohydrates. I really should haven't written that without saying DRIED beans. My bad. But I just assumed that most people aren't really ever getting that many undried beans, especially if they are eating refried beans like you mentioned. I'm amazed that you don't get gas from refried beans. Unless you are eating beano or something.

          Regardless, I get gas everytime I eat dried beans. Everyone I've asked does.

          Both of us appear to be talking a little too generally, but just to name a bean that is equally high in carbs as it is in protein is soy.

          Now on a more arguing side of things: What mislead you into thinking that the same amount of protein and carbs have to be in the food? Can you even name any foods that have more proteins than carbs besides meats? I can think of 2 right off, soybeans and peanuts. And both are beans, imagine that.

          I don't just read crap and regurgitate it. I've been using food combination and other natural methods to bring myself to good health, and not specifically, but since it's part of our discussion, I've also used them to get rid of gas. Maybe I'm more inclined to having gas than other people or something, but food combination has worked quite well for me. But I don't have an intestine full of impacted unhealthy foods either, so maybe that also attributes to my not getting gas from using food combination.

          Personally though, I can't see how you can argue with rule #1. It's pretty freaking straight forward. Carbs dont break down in acid.
          • I guess "beans" is too general a term.

            I've tried food combination myself, and some of it works, some of it doesn't really make a difference. The mixing carbs and proteins rule didn't really didn't make a difference for me, and I've found plenty of "health experts" who contradicted the rule and said it was fallacious. To eat all meals completely devoid of either carbs or protein doesn't make sense to me. I would be malnourished if I did this. Even the vegatables I typically eat have both protein and carbs.

            There are some parts of food combining that are true for me. For example, if I eat bananas and oranges together (sweet fruits and acid fruits), I usually have indigestion.

            I guess whatever works for you. Everyone's diet needs are different. I just can't imagine life without beans.
            • Like the other guy stuck me with, it's not just proteins and carbs, it's concentrated. If those foods get processed, cooked, or when some of them are dried (like beans) they become a concentrated protein or carb. Pasta is a concentrated carb. Table sugar is a concetrated carb. Dried beans are concentrated proteins and carbs. And so on.

              Not that you're suppose to eat as much unconcetrated proteins and carbs as you can fit into your stomach either though.

      • If you dont eat carbs protien goes straight to fat instead of muscle forming, all atheletes and bodybuilders know that.

        Carbs must ALWAYS be consumed with Protien and Fat.

        Now its true eating all 3 together give you higher chance of having gas, but whats better, having gas, or being a blimp without gas?

        Eat just carbs alone and you'll be as fat as a sumo, Eat only protein and your body will burn muscle for energy as it adapts to this, Eat a balanced diet of all 3, with each meal, and youll be fine.
    • They are working on it, Here is the CNN article: Researcher looks to take the bad out of bean eating [cnn.com]
    • There is an actual measurement of sort by environmentalists which calculates the total volume of flatulent gas produced by cows over a specified region, i.e. either a state or country. The methane complex supposedly influences the lower atmospheres and stirs up the Greenhouse Effect.
  • Maybe this will solve the mystery of Ramen noodles not ever filling me up, no matter how much I eat...

    Yet..., I continue to eat it.
    (just finished some)

    I don't know what i'm saying, i'm drunk...

  • And plenty of code space for more. (Score:3, Interesting)

    by Rhinobird ( 151521 ) on Sunday May 26, 2002 @07:44AM (#3586731) Homepage
    If I remember my high school biology correctly, there are 4 nucleotides, and it take 3 of them to encode an amino acid, basic math...4*4*4=64. We earthlings aren't even using half the code space provided by our current DNA system. Just 1 more and we're there at half.
    • Ah, but they are already taken. Like the IP-numbers of the old days.. Nature thought it wise to build some redundancy. Some popular amino acids have multiple encodings, so mutations can be meaningless. Plus you have the stop-codon of course.

      I think an UTF8-like scheme would be safer, for future enhancements and the like.
    • sorry, my reading is bad...i thought he said 31st known amino acid instead of 22nd. Hoo boy do I need some sleep.
    • The codon (or group of 3 nucleotide IIRC) maybe don't code for an amino acide and may have other signification. You are assuming that those codon not translated in amino acid are useless. How about "stop" ? or "Repeat" ? "or start copy now" ? Note : I am not a biologist so what is above maybe totally wrong.
    • The thing is, tRNA is only really specific for the first two bases in a codon. The third base can "wobble." For example, alanine can be represented in the genome by GCU, GCC, or GCA. This is because the anticodon (IGC) uses inosine to match the third base, and inosine can pair with uridine, cytidine, or adenosine. Only a couple of tRNAs require all three bases to match, like the tRNA carrying tryptophan.
      • The thing is, tRNA is only really specific for the first two bases in a codon. The third base can "wobble." For example, alanine can be represented in the genome by GCU, GCC, or GCA. This is because the anticodon (IGC) uses inosine to match the third base, and inosine can pair with uridine, cytidine, or adenosine. Only a couple of tRNAs require all three bases to match, like the tRNA carrying tryptophan.



        mmmmm...tryptophan.... tryptophan => tryptamines => fun dreams
    • because it didn't tell us *which* codon they were working with. There are several codons which were understood to be interepreted as STOP signals, so based on this fragment of the article,

      "Surprisingly, the codon Krzycki's team identified should have signaled a stop to protein building but it did not."

      it must be one of those. They previously-known-to-be-stop codons are: UAA, UGA, and UAG (did I miss any?). So which one is it? If you know, please reply to this post.

      For reference, here [ultranet.com] is a good page for more info on codons, their product amino acids and more.
      • Looks like you're right about it being a stop codon. Actually, the article does tell you which one (in jargon):

        "Then in 1998, they published a paper showing that the gene had a component called an in-frame amber codon that behaved unusually."

        "Amber" = UAG

    • Yes, yes there are 64 possible amino acid encodings. However, by only yielding 22 possible amino acids, the system provides a level of redundancy. The redundancy usually occurs around the third nucleotide, for instance, Ser can be coded AGU and AGC. This redundancy compensates for "point mutations", mutations that effect only one nucleotide. Because of the redundancy of the genetic code, the effect of point mutations is reduced by about 1/4. From looking at the old Codon Table [pangloss.com], it is clear that the new amino acid was coded by UAG (the "amber" discussed in the article). However, UAG obviously stops for some organisms (Scientists dont make things up), so perhaps UAG stops unless the complementary tRNA can be found? If this is the case, then it is likely that all three if the "stop" codons code for certain new amino acids in some organisms. The trick, of course, is finding them.
      • This is exactly what happens with UGA for selenocysteine. If you have a selenium deficiency, then the proper tRNA isn't synthesized and the ribosome stops translation like normal.

        Incidentally, while the genetic code is pretty much universal, there are some variations. For example, in mitochondria, instead of functioning as a STOP codon, UGA encodes for tryptophan; instead of coding for isoleucine, AUA encodes for methionine; instead of coding for arginine, AGA and AGG function as STOP codons.

    • This "new amino acid" is coded for by a triplet that formerly was only observed to be a stop codon. That is, when the translation machinery came upon the base sequence on the RNA it was reading to build the peptide chain, it ended the chain.

      Now consider this. What if the cell produced the matching tRNA and associated "new amino acid" only intermittantly. When it was available, this stop-codon wouldn't be a stop codon at all and translation would continue, but when it was missing, translation would stop.

      This raises another interesting question (that may already be answered). Some organisms can not synthesize all the amino acids and must obtain some of them from dietary sources. These amino acids are referred to as the essential amino acids for that organism. If their diet is deficient in these essential amino acids, they can't make all the proteins they need, and bad things generally happen.

      So, the question is, what happens at a translational level in this situation? Does translation just stop, leaving shorter peptide chains? Are their situations where the products of partial translation have biological activity?
    • come on now, 64?

      EVERYONE knows the number they're looking for is gonna end up being 42. every other pair will be unstable, and the meaning of like will be proven to be 42. and douglas adams will rise from the grave and lead us to salvation.
    • Except we're using all of them. The codings are here [ultranet.com]. There are 20 amino acids used by the vast majority of cells, and most of these are encoded multiple times.
    • Actually, there are a certain number of redundencies... not sure if its cause they're built in, or there are just two or three different ways to make a certain protein...

      Also, IIRC half the codespace is taken up by the left/right dichotomy... Each amino acid can be left/right, but for some reason all of them are right-handed. The tRNA that decodes the DNA must convert all of the code sequences to right-handedness as it builds amino acids. That way, you can decode EITHER half of a DNA strand and get the same results...

  • I'll take "Reasons I Majored in Engineering" (Score:4, Funny)

    by Dolly_Llama ( 267016 ) on Sunday May 26, 2002 @07:44AM (#3586732) Homepage

    for $500 please Alex

    ...What is Organic Chemistry.

  • Ok, I looked everywhere for details, couldn't find any. I don't have a science-subscription. What's the structure? Only info mentioned is that it at 1st looked like lysine.



    BTW, there are many variations of amino-acids known, all made by post-processing. There are still only twenty directly coded for in DNA, AFAIK. This looks like something in-between, coded for by the stop-codon, but somehow this one is treated special.

    • Looked a bit further.. There are two structures deposited in the protein data bank [rcsb.org]: 1L2Q and 1L2R. But alas, they're not available yet, 'release on publication'.

    • 21st amino acid (Score:3, Informative)

      by aswang ( 92825 )


      The amino acid they discovered in 1986 is selenocysteine, which is also encoded for by a STOP codon (UGA in this case). Maybe there is an entire class of amino acids that are encoded in this manner, in between the 20 directly encoded amino acids and the multifarious post-translationally modified amino acids (e.g., hydroxyproline and hydroxylysine in collagen; gamma-carboxyglutamate in various clotting factors)


      And you probably need more than just a STOP codon to incorporate pyrrolysine. With selenocysteine, you need enzymes to convert the serine residue on the tRNA to selenocysteine, an enzyme to activate the inorganic selenium, and a modified translation factor that recognizes this special case.

      • Re:21st amino acid (Score:4, Funny)

        by texchanchan ( 471739 ) <ccrowley@NosPAm.gmail.com> on Sunday May 26, 2002 @08:13AM (#3586780)
        Re, ...selenocysteine, which is also encoded for by a STOP codon ....

        This sure sounds like a kluge. Who designed this system, anyway? They need to clean up their code.
        • Re, ...selenocysteine, which is also encoded for by a STOP codon ....

          This sure sounds like a kluge. Who designed this system, anyway? They need to clean up their code.

          It's called redundancy, man. That's when god decides to play her cards right, in case she dies/retires early.

        • Re:21st amino acid (Score:3, Insightful)

          by aswang ( 92825 )
          Evolution is all about kludges and supporting legacy operating systems. The genetic code is pretty much completely backwards compatible back to the most ancient prokaryote (though I'm not sure if it's completely the same in the archae kingdom) Nature also often ends up reusing code for completely unrelated purposes. And Nature never, ever throws away legacy code until she really, really has to. There are all sorts of non-working remnants from millions of years ago still floating around in our heterochromatin. And yet, for us humans at least, everything seems to fit in under 3 GB, including all the bloat and non-working code.
      • Ah, thanks for the info! Found some more here [okstate.edu].

        The extended numbering (21st, 22nd) for this class sounds a bit unwarrented to me though. Although I can see the PR-perspective...

      • Re:21st amino acid (Score:1, Informative)

        by Anonymous Coward
        The key point about amino acids 21 and 22 is that, in contrast with post-translational modifications, the residues are fully formed before their addition into the protein. True, selenocysteine is modified after it has been attached to the tRNA, but many organisms do this for the formation of some of their 'normal' amino acids as well. (Pyrrolysine may be formed in this way as well, but it is yet to be determined.) Pyrrolysine has its own, dedicated tRNA (which is most of the focus of one of the two papers). So these two are encoded directly in the DNA of the gene, rather than being subject to other modifications. It doesn't seem to be known yet whether selection of this amino acid is position dependent, like selenocysteine, or fully substituted in this species of bacteria.

        Proposed structure of sidechain is:
        -CH2-CH2-CH2-CH2-NH-(C=O)-C5-C4-X
        where C5 and C4 are part of a pyrrol ring (5-membered, N at position 1, double bond N1-C2) and X is listed as CH3/NH2/OH - not clear if they mean it is variable or as yet uncertain.

        Interesting to note that, even at final year college level, they still go with the "There are 20 genetically coded amino acids" dogma.
      • In the Science article [sciencemag.org](subscription req'd), they mention that the nucleotides surrounding the triplet codon recognition sequence are also semi-conserved - so the tRNA sequence recognizing the mRNA might be more like CUCUAA binding in a non-standard way instead of a simple triplet interacting with a codon. This could provide a higher level of specificity for incorporating these "specialized" amino acids like pyrrolysine or selenocysteine.

        Also, the UGA stop codon is a good choice, since the ribosome will pause there longer than the typical amino acid coding sequence and it also has a higher readthrough probability than other more efficient stop codons - both of which are helpful for more involved tRNA-mRNA interactions.

    • genetic code non-universal (Score:4, Interesting)

      by BlueboyX ( 322884 ) on Sunday May 26, 2002 @10:24AM (#3587048)
      Oddities in the genetic codes of different species have been observed before. While all known life froms have very similar genetic codes (this codon yields that amino acid) there have been some life forms that are exceptions. Several kinds of bacteria express a different amino acid for a specific codon than, say, a human cell would.

      So finding a bacteria like what this artical describes is only a mild suprise.

      Great detective work though. Alot of people would have decided it was alot easier to call this an abberation than to spend ~2 years finding out what was really going on.

    • The structure of most of the amino acids is very similar, they vary only in one group bonded to the central carbon atom. The other three groups (H, amine and carboxylic acid) are constant.

      Pyrrole is a five membered aromatic ring with 4 carbon atoms and one nitrogen atom.

      The name pyrrolysine sugests that pyrrole might be the fourth group bonded to the central carbon atom.(But thats just a guess on my part)

      If it is pyrrole bonded to the central carbon atom then there are three ways in which it could do it: (1) to the nitrogen (2) to one of the the two carbon atoms closest to the nitrogen (3) to one of the carbon atoms furthest from the nitrogen. Again it would just be a guess on my part as to which of these it is.

      Tom.
  • Does this bring us a step closer to figuring out how life on Earth started? If I recall right it's about building amino acids out of smaller chemicals, and living organisms out of that.
    • Does this bring us a step closer to figuring out how life on Earth started?

      Save yourself some time-

      Between The Hitchhikers Guide to the Galaxy and Monty Python's "The Meaning of Life" you will find this, and many other such questions, covered.

  • Importance of this discovery? (Score:5, Interesting)

    by donnacha ( 161610 ) on Sunday May 26, 2002 @07:55AM (#3586750) Homepage


    The very fact that this amino acid was overlooked for so long suggests that it's direct importance to our lives is negligible; it's relevance is more about filling the final gaps in an overall picture.

    In the article [osu.edu], Krzycki suggests that it also alters the way we should approach genetics:

    "This shows us that the genetic code, and therefore, evolution is much more plastic than people might have thought."

    "I think this work will cause researchers to start looking at genetic sequences that they might have thought at first were simply aberrations," he said. "Instead, they might signal discoveries like ours."

    • The very fact that this amino acid was overlooked for so long suggests that it's direct importance to our lives is negligible; it's relevance is more about filling the final gaps in an overall picture.

      That is assuming of course that our current picture is accurate. Don't forget that for the most part our understanding in science is not based on absolutely insoluable facts yet simply the available facts at the time.

      While this AA may not be a huge player I wouldn't simply dismiss new discoveries based on that line of thinking.
    • How is it not important? I don't understand. For years people thought acne was small worms crawling out of the skin. (I have in my possesion an early 1800's medical book that actually has drawings of it.) We think that is now a silly thing, but it was reality to them.

      Perhaps we might finally learn more about body parts that we currently slice out of children if the parts are infected. Perhaps these new aminos hold clues to diseases.

      Although we may not know the application now, even the most "insignificant" discovery can change the world.


      • Perhaps these new aminos hold clues to diseases.

        So far, as I understand it, this 22nd known amino acid has only been found in methanogens although the article [osu.edu] states that:

        Krzycki believes it is likely to be found in other situations - in other organisms

        Those other organisms have yet to be identified and almost certainly don't include humans. That suggests that this discovery won't have much bearing on diseases that affect humans, unless it's an important factor in the make-up of one of our parasites.

        • ... Those other organisms have yet to be identified and almost certainly don't include humans. ...

          Your reasoning escapes me.

          Finding something that is quite rare in one place generally makes it much simpler to detect in other places. Often you wouldn't have found it before merely because you had no idea as to what you were looking for. (Or at least, you weren't looking for it.) I would expect that there are many small chemicals that occure rarely, but are necessary for the proper functioning of the human body, yet have not been detected.

          To pick an example that's a bit old now: Selenium is a poison. It kills animals (and makes plants sick). But without a bit of selenium we die. This was found out only when sheep in Austrailia started getting "milky white disease". Austrailia may be the only area of the world that is low enough in selenium for this disease to reveal itself. We don't need much selenium at all. But the tiny amount that we do need is vital.
    • The importance of this, if it holds out in other organisms, is that we usually look for an "Open Reading Frame (ORF)" when identifying many new genes... this ORF is defined as a stretch of Amino Acids (coded by DNA) without any Stop codons (there are three stop codons (three letter triplet)) As soon as we see a stop codon, we usually stop. IF this is indeed a new amino acid coded (sometimes) by one of these stop codons, we will have to look back at how we call genes. Some of the genes may be longer than we think.

      However, this is probably a very, very rare occurence and it could be that this only happens in a small subset of organims, meaning that it will have no effect on Humans or most other relevant "model systems"

      Nonetheless, this is very cool :)
    • It depends on what you mean by "direct importance," I suppose. After all, it's quite possible to live a long and happy life without knowing any basic science whatsoever.


      Still, while pyrrolysine may only be relevant to methane-producing bacteria, the similarly stop-codon encoded amino acid selenocysteine is incorporated into a couple of important enzymes like glutathione peroxidase (which keeps your red blood cells from lysing from oxidative damage) and 5'-deiodinase (which is important for regulating the activity of your thyroid hormone). Who knows what role the translation machinery plays in the etiology of diseases like hemolytic anemia, and hyper- or hypo-thyroidism?

      • Clinically speaking, there are many other causes of hemolytic anemia that are much much more common than anything involving the translation machinery at the level you're describing. It's also the same thing with hyper- and hypo-thyroidism. I'm not saying you're wrong and these things couldn't cause those diseases, only that they would be relevant in a tiny minority of cases.
    • Specificially of the Methanosarcina? If so, then yes, this has direct implications to your health :-) Otherwise, it more interesting from the standpoint of evolution as Methanosarcina is an archaeon (a member of the Kingdom Archaea, a group of prokaryotes that appear to be more closely related to you and me than to the superficially more similar bacteria).

      However, the very related nature of the Archaea to the the eukaryotes like us suggests that it is not completely unlikely that pyrrolysine will be found to occur in small amounts in human proteins. The 21st amino acid, selenocysteine, occurs in only a handful of known human proteins but is extremely important where it occurs.

      It's been an exciting few weeks for those of us interested in the Archaea. A few weeks ago, the smallest genome of a known free living organism, whjich happened to be an archaeon, was sequenced, and now this.
    • "This shows us that the genetic code, and therefore, evolution is much more plastic than people might have thought."

      "I think this work will cause researchers to start looking at genetic sequences that they might have thought at first were simply aberrations," he said. "Instead, they might signal discoveries like ours."

      Or maybe people already know that. It's already well established that different organisms use different translation tables when synthesizing proteins. The NCBI [nih.gov] lists 17 [nih.gov] such tables in their section on gene transltation. Heck, the human nucleus and mitochondria use different translatation tables! Is it really such a surprise that those differences might occasionally include an additional amino acid?

  • Bah. (Score:3, Funny)

    by NoMoreNicksLeft ( 516230 ) <john.oyler@noSpAm.comcast.net> on Sunday May 26, 2002 @07:55AM (#3586751) Journal
    The X-files already taught us there were more amino acids to be discovered. I just hope they find the 5th and 6th nucleotides again, so that there will be proof of extraterrestrials.

    And whatever you do, don't let the smoking man get ahold of them, that's how they dissappeared the first time around. And no, he isn't dead. He obviously had the black army/CIA helicopters stage his death. What a drama queen.
    • But it took that scientist about 2 days (or less!) to find those nucleotides. It took these guys 2 years.

      Maybe in X-files land she wasn't just a random scientist, but someone actually in the know. That is why she had to die in that episode; she could have become a major security risk.

      Just building new and more creative x-files conspiracy theories. :>

    • We all know it was a clone of the smoking man that got killed! Duh!!

  • Learn a bit (Score:2, Informative)

    by Anonymous Coward

    There are lots of information sourced from documents at this [qmw.ac.uk] page.

    Maybe the discover will revolutionize the way humans feed - should help French vine to be even more flavorful too? :)

  • Creating *new* bases (Score:5, Informative)

    by HorsePunchKid ( 306850 ) <sns@severinghaus.org> on Sunday May 26, 2002 @09:08AM (#3586859) Homepage
    There was an article in Science News [sciencenews.org] a year or so ago that described some research on the topic of making DNA code for new bases. Apparently it's somewhat of a mystery why all life has "chosen" to use the same set of amino acids as a basis. With 64 codons, one would expect to be able to code for 64 different amino acids, but there's some redundancy that allows for some error tolerance. It turns out that there are some branches of life (maybe the Archea or something, I'm not sure anymore) that actually use bases that don't appear in any other organisms. So that spurred researchers to see if they could take some other amino acid that isn't used (something other than the familiar GATC, etc.), and make functional DNA with it. I don't remember exactly how far they got with it, but I believe they essentially had a functioning bacterium. (Whether it could reproduce or not, I'm not sure.)

    Ah! Here's the original article: Code Breakers [sciencenews.org]. It's definitely worth a read.

    • The technique used to create a new base reminds me
      of an MIT trick reported in Steven Levy's book HACKERS.

      One fine midnight, the hackers snuck into the comptuter room where the first transistor based
      computer resided. A few minutes with a soldering iron and the computer had a new opcode.

      The DNA scientists were not changing the DNA code so much as they were changing the cell's compiler . The DNA didn't change, only one of its codons were now interpreted as a different amino acid.
      • Perhaps the comparasion is more apt than you have made it out to be - remember, the new instruction didn't cause the hacker who did it any problems, but it trashed the work of another user of that system - she ran some programs that depended on a particular path, and they corrupted it.
        Sure, they *thought* they had covered all their bases, but they hadn't.
        It's not nice to fool with Mother Nature.
    • While we don't really know why the genetic code is for the most part universal, it's probably dictated by thermodynamics and natural selection. The 20 amino acids we have are all pretty much readily synthesized from glucose--pretty much the common fuel for all life--and its metabolites. So ultimately this would limit the different permutations of carbon atoms.

      And while the genetic code is pretty universal, mitochondria use a slightly modified version, and according to the article, Salmonella have tRNAs that recognize four bases instead of just three.

  • Metaphysical Towers (Score:3, Insightful)

    by Alien54 ( 180860 ) on Sunday May 26, 2002 @09:11AM (#3586867) Journal
    This is sure to throw a monkey wrench into the speculations of folks who have built metaphysical towers based on the number 21 [digital.net].

    Even more so now that researchers are looking for numbers 23 and 24.

    Strange stuff indeed. That is the problem with this class of metaphysician. reality intrudes from time to time.

  • Infinite number of amino acids (Score:3, Informative)

    by redelm ( 54142 ) on Sunday May 26, 2002 @09:42AM (#3586942) Homepage
    It's elemenary organic chemistry. An amino acid is nothing more than an alpha amino carboxylic acid. R - CHNH2 - COOH . R can be any of an infinite number radicals, but interestingly only 20 or 22 are found in life. And only the levorotary form at the amine carbon is found.

    Nor is it obvious why certain radicals are vital, and most are not. Some of the common radicals are missing in the vital amino acids. Hydrogen and methyl are there, but ethyl, propyl and higher n-alkanes are not. Yet isopropyl, and both 1 & 2-methylpropyl are. Wierd. Perhaps it has something to do with the way exclusionary mechanisms to keep undesirably amino acids out of the protein building machinery.

    From an information-theory viewpoint, why are the DNA sequences largely incompressible? Are the three-base pair codons (6 binary digits each) equally probable? Those codons could be decoded into 64 possibilities, yet we have only 22 amino acids. Are some of the codons used for amino acid pairs? Or else we've got alot of missing acids. Untils those codons are themselves decoded (and any bigrams, tridgrams, etc), we should expect surprises. And what of the great expanse of alleged junk? Does nature have a signal-to-noise ratio approaching that of USENET? :)

    • Well put. There is of course the need for the masses to know 'the truth' that they are sure is out there just being abused by dark powers. Whether geoid theory in the face of plate tectonics or the current state of molecular biology there is an irrational, fear driven need to have one town crier or another, in or out of the press, proclaim the final truth, and, thus the fear that drives religion demands ultimate answers from science which is a process and probes without ever stating ultimate answers.
    • And to throw a spanner in the neatness theory, one isn't optically active at all (Glycine) and one is not strictly an amino acid (its an imino acid).

      And for those who like R and S notation, one is neither, and two are S whereas all the others are R. (Sulphur is a higher precedence than Oxygen).

      • Yep, spot on except that you wouldn't expect glycine to be optically active because it doesn't have a stereogenic centre - the R group is a hydrogen.

        And as for the sulphur, damn those Cahn-Ingold-Prelog precendece rules!

        Elgon
    • >And what of the great expanse of alleged junk? Does nature have a signal-to-noise ratio approaching that of USENET?

      Nature's is either a little lower or much higher, depending on how much of living matter you consider "signal".

      --Blair
      "See, here is where having Steven Jay Gould around would help..."
    • The short explanation for why only L-amino acids are found (except in bacterial cell walls) is that all the enzymes required for translation (and for the most part, all enzymes in general) are stereospecific--the substrate has to fit in the binding cleft the same way only your left hand can really fit into a left glove.

      As for why only certain R groups are found, it's probably ultimately dictated by thermodynamics, with a little input from natural selection. Nature is very conservative with the building blocks it uses, and almost all of the amino acids used can be derived from glucose and its various metabolites. n>2 alkanes R groups would probably require a lot of energy to synthesize, particularly since they're hydrophobic and all these reactions happen in an aqueous environment. If you can't make it from glucose within the thermodynamic constraints of a biological system, you're unlikely to make it.

      Probably because of thermodynamics as well, not all codons occur with equal probability. And because of the thermodynamic instability of the third base pair with regards to codons/anti-codons binding, many tRNAs are only specific for the first two bases (a phenomenon known as "wobble")

      Because of thermodynamic and steric considerations, it would be difficult for ribosomes to accept dipeptide/tripeptide tRNAs, since the active sites on the enzymes have only so much leeway as to where they expect to physically find the atoms they're supposed to act on. While theoretically an alternate translation system could evolve, given the conservative nature of evolution, it would probably take a long time and require severe selective pressure.

      Finally, as for "junk" DNA, a lot of it has been found to serve various structural functions with regards to the integrity of the genome. There are probably very few regions of even heterochromatin that don't have a function, and the sequences that are truly useless now probably had a function in the evolutionary past.

    • Re:Infinite number of amino acids (Score:4, Insightful)

      by IdahoEv ( 195056 ) on Sunday May 26, 2002 @01:57PM (#3587718) Homepage
      but interestingly only 20 or 22 are found in life. And only the levorotary form at the amine carbon is found.


      At the risk of nitpicking, significantly more than 20 or 22 amino acids are found in life, just not as building blocks of proteins. Take for example dopamine, which is an amino acid not used in proteins in any known organism, but a rather common neurotransmitter in most animals.


      • Actually, much more than 20 or 22 are found in proteins, they're just not genetically encoded. This basically means that the protein is made with a certain amino acid in that spot, and it gets converted later. One of the classic examples is hydroxyproline, which is a modified version of proline (the only amino acid that's technically an imino acid). There are lots of hydroxyprolines in collagen, and conversion of proline to hydroxyproline is vitamin C dependent. So if you don't get enough vitamin C, you have lots of defective collagen which leads to teeth and hair falling out when you have scurvy.

        The significance of the whole 22nd amino acid thing is only that it's the 22nd GENETICALLY ENCODABLE amino acid found in nature, and it's in some weird bacteria, not in humans. This means that it has its own tRNA. There are more than 22 amino acids found in proteins, even in humans, and in the lab they've created "alien" bacteria that use two or three completely artificial amino acids to incorporate fluorescent tags into protein molecules and that kind of thing.
  • In the "new stuff about amino acids" department, several researchers have recently discovered that there is a fifth taste in addition to sweet, sour, salty and bitter. It has been called umami [nature.com] and has been extensively researched at Howard Hughes Medical Center [hhmi.org]. Naturally the Japanese have established a whole new research center on this at SRUT [iijnet.or.jp] (Japanese character module required) so can a special edition of Iron Chef [ironchef.com] be far behind?
    • several researchers have recently discovered that there is a fifth taste in addition to sweet, sour, salty and bitter. It has been called umami

      That's really funny. Umami is a japanese word, meaning approximately "yummy" or "delicious" in english. So now there's sweet, sour, salty, bitter, and "mmmm....".
    • The fifth taste is not a recent discovery, ok maybe to some researchers it is.

      The Japs have known about it for a long time - hence MSG.

      It's probably more like people are doing more and deeper research into it.

  • Building blocks (Score:3, Informative)

    by Herger ( 48454 ) on Sunday May 26, 2002 @12:30PM (#3587439) Homepage
    It's not surprising that there are tRNA's in rare organisms that encode for "non-standard" amino acids -- evolution just selected against them, since the common 20 are so prevalent and easy to produce or obtain from food. Humans actually use 22 amino acids, but two of them are not genetically encoded, but produced by modifying the finished protein (hydroxylation of proline and lysine during collagen biosynthesis. Rice and beans are not sufficient, you need vitamin C to make collagen) Some bugs live in places where "non-standard" amino acids are probably preferred to make proteins more suited to the enivronment -- extreme conditions like Antarctic ice, or thermal vents.

    It's important to remember that amino acids aren't the only building blocks -- cell membranes are made of lipids, cholesterol, and polysaccharides (sugars). There are many possible modifications beyond the amino acid sequence. For instance, immune markers (blood type, etc.) are sugar chains which are tacked onto proteins. Sugars on the surface of viruses help them bind to cells. Another common modification is phosphorylation: addition of phosphate to a protein, which is a common method of activating (or deactivating) proteins.

    The body also uses lipid derivatives, steroids, and most importantly vitamins to obtain chemical functions not provided by amino acids (catalysis, cell signaling, etc.)

    • Re:Building blocks (Score:2, Interesting)

      by aswang ( 92825 )
      The 21st amino acid, selenocysteine, while rare, is actually integral in synthesizing important eukaryotic enzymes like glutathione peroxidase (necessary for the stability of red blood cells) and 5'-deiodinase (necessary for regulating thyroid function).


      What is remarkable about selenocysteine and pyrrolysine is that they are actually encoded by the genome. This is in contrast to hydroxyproline and hydroxylysine (and gamma-carboxyglutamate, necessary for blood clotting) which are encoded by standard proline, lysine, and glutamate codons. It's not until the peptides are being modified in the endoplasmic reticulum and Golgi apparatus that the hydroxy- or carboxy- groups are added on.

    • It's not surprising that there are tRNA's in rare organisms that encode for "non-standard" amino acids -- evolution just selected against them, since ...

      You can't really claim that they were selected against unless you can demonstrate that they were once more common. They could be emerging.

      And, to be a bit nitpicky, you can't really claim that they were selected against unless you can demonstrate that they were what was selected against. Frequently an emergent gene occurs in an animal that for totally separate reasons is unfortunate. I suppose that you could claim that the dinosaurs were selected against, because they weren't immune to being hit on the head with a meteor, but that's hardly fair. And it won't be fair until long after we have taken steps to guard ourselves against the same fate. (Even then, I'm dubious.)

      • Re:Building blocks (Score:2, Interesting)

        by Herger ( 48454 )
        You've got a point there, there is no evidence to suggest that they are selected for or against. In fact, it's possible that there could be as many as 30 amino acids genetically encoded. This is just a WAG, of course; 4^3 possible codons, but if you consider the last base to be a "wobble" base in every codon (i.e., purine or pyrmidine), that cuts it to 32, then you have a start and stop codon, cutting it to 30 (even this depends a lot on your tRNA's).

        Frequency distribution of codons show that some codons are simply more common, and some amino acids can be coded 6 ways (e.g. serine) while there's only one way to code methionine. I suggested selection because the most likely way that this distribution occured was mutation of tRNA's and aminoacyl-tRNA synthetases for uncommon amino acids, which implies genetic selection. There's a raft in literature on genetic evolution I'm not familiar with though (have to admit I got a "C" on my paper about that)

        It's possible to substitute synthetic tRNA's in the lab to insert non-standard amino acids -- no reason it's doesn't happen in nature, all it would take is a "mutated" (from the point of view of the codon table in Voet and Voet) aminoacyl-tRNA synthetase to attach a different compound to the tRNA. It would be interesting to study whether this was conserved since the beginning of time or emergence of a new pathway.
  • For humans and most other higher species, there are 20 amino acids found in proteins. The 21st and 22nd, as far as this scant article seems to imply, are found only in certain types of bacteria.

    Amino acids are encoded from triplets of DNA, called codons. 4^3 equals 64 possible codons. In our cells, there are 64 types of tRNA, each of which binds to a particular codon, and maps to one of 20 amino acids, plus "start" and "stop".

    Now if someone found a human cell type which contains an altered tRNA that encodes for a non-standard amino acid, then THAT would be big news for us... e.g. major revisions to Biochemistry 101 texts.

    Finally, only 12 of the 20 amino acids in our body are "essential". The other 8 can be synthesized from other similar amino acids. Hence, the combination of beans and rice doesn't necessarily contain all 20 amino acids, but at the very least, it has the 12 essential ones.

  • It's not about the amino acid, it's about the tRNA (Score:5, Informative)

    by ZanshinWedge ( 193324 ) on Sunday May 26, 2002 @01:49PM (#3587680)
    It's very difficult to glean the details of the paper from the abstract alone, but I think I know what's going on. Firstly, this is *not* the first discovery of a non-standard amino acid in nature. There are several rare amino acids that are used by various organisms (usually bacteria) that are not in the "official" registrar of 21 AAs. However, in those cases the amino acid is simply a stand in replacement for a very similar amino acid. Essentially the only thing that need to be changed in that case is the enzyme that produces the amino acid.


    This case is special not because of the use of a non-standard amino acid, but because it is an *additional* amino acid rather than a replacement. This means that the machinery of translation of an RNA codon to an amino acid (via tRNA) and the construction of the amino acid (via an enzyme) exists in parallel with the machinery for all the other existing amino acids. This is remarkably interesting because it represents a much larger genetic difference in the amino acid translating machinery, and a difference which we have never seen before.

  • if they investigate the freshly discovered ice masses on Mars, I wouldn't be suprised at all if numerous other amino acids are discovered.

    just a thought


    BOFH_org

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