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New Amino Acid Discovered
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.
Time for suppliment companies to make a quick buck on a new protien
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a way to help people naturally prevent the farts caused by all the good food we're supposed to be eating. Instead of taking a beano with the meal, I'd rather have a daily magic pill or gene therapy to prevent all that nasty, stinky gas.
Steve Magruder, Metro Foodist
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...
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.
If Mr. Edison had thought smarter he wouldn't sweat as much. --Nikola Tesla
for $500 please Alex
...What is Organic Chemistry.
Somewhere, something incredible is waiting to be known. -- Carl Sagan
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.
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.
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Cruise TT
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.
C. Sagan : A demon haunted world:
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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, 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 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.
There are lots of information sourced from documents at this page.
Maybe the discover will revolutionize the way humans feed - should help French vine to be even more flavorful too? :)
Our supplement formula is comprised of the highest quality crystalline protein source
:) j/k
10 bucks says I know whats in his clipboard
slashdot: where everyone yells sarcastic metaphors to themselves to understand the issue
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.
Bah... that's the sort of thing that FOOD eats!
NEW AMINO ACID DISCOVERED; FUNDAMENTAL BUILDING BLOCK OF LIFE
COLUMBUS, Ohio - Two teams of researchers from Ohio State University reported today that they had identified the 22nd genetically encoded amino acid, a discovery that is the biological equivalent of physicists finding a new fundamental particle or chemists discovering a new element.
Two papers describing the discovery appear in the current issue of the journal Science. Prior to this, scientists had believed that there were only 21 natural amino acids -- the key building blocks of proteins.
For 30 years after the discovery of the structure of DNA and the unraveling of the genetic code, scientists believed that there were only 20 natural amino acids. Then in 1986, researchers broke that numerical barrier announcing that the 21st had been discovered.
Finding a 22nd suggests that even more of these basic biological building blocks may be found using modern genome sequencing techniques.
The discovery grew out of some very basic biochemistry examining how a particular type of microbe - methanogens - can convert methyl-containing compounds into methane. While researchers have long understood the biochemical mechanisms for how acetate and carbon dioxide are converted to methane, they didn't understand how a common class of compounds - the methylamines - are transformed into this gas.
One research group, led by Joseph A. Krzycki, an associate professor of microbiology, had been working for several years with a particular strain of microbe, Methanosarcina barkeri. This organism, a member of the recently identified domain Archaea, is able to convert monomethylamine, dimethylamine and trimethylamine into this greenhouse gas.
Krzycki's research group had isolated specific proteins related to the process in 1995 and, two years later, they had isolated and sequenced one of the genes responsible. Then in 1998, they published a paper showing that the gene had a component called an in-frame amber codon that behaved unusually.
Codons are three-letter "words" identifying the bases DNA uses to specify particular amino acids as building blocks of proteins. Normally, codons signal the start of a protein, its end or a particular amino acid used to construct it. Surprisingly, the codon Krzycki's team identified should have signaled a stop to protein building but it did not.
"Joe and his colleagues found this happening in genes important for all three of the methylamine compounds - something that wasn't supposed to happen," explained Michael Chan, an associate professor of biochemistry and chemistry at Ohio State. Chan led the second research team that identified and determined the structure of the amino acid.
The realization of the codon's odd behavior suggested the possibility of a new amino acid, but the researchers knew there might be other explanations as well. Krzycki and his colleagues sliced the protein into smaller bits called peptides, and began sequencing them, a process which usually ultimately reveal the amino acid responsible for the protein.
"That all seemed to point to this being just lysine, one of the normal amino acids," Chan said. Regardless, Krzycki asked Chan and Ph.D. student Bing Hao to start working on deducing the crystalline structure of the protein containing the amino acid. At the end of the two-year process, Hao and Chan had determined the structure of the protein, part of which revealed a new amino acid.
At the same time, Krzycki was looking for other evidence. He, along with doctoral students Gayathri Srinivasan and Carey James, was eventually able to identify the specific transfer-RNA (tRNA) needed to insert the new amino acid into protein, as well as another important enzyme essential to the process. These two discoveries, along with the detailed crystalline structure, convinced the teams that they had found a new genetically encoded amino acid -- pyrrolysine - the 22nd known to science.
"We realized that we had to know which tRNA would decode that amber codon," Krzycki said. "Finding it was an essential part of the puzzle."
He believes this will be a very rare amino acid, given the fact that it has taken so long to identify it. However, Krzycki believes it is likely to be found in other situations - in other organisms - aside from methanogens. He's philosophic about the importance of the discovery: "This shows us that the genetic code, and therefore, evolution is much more plastic than people might have thought."
Chan agrees, pointing to the strong possibility that finding a 22nd genetically encoded amino acid should stimulate the search for a 23rd or a 24th. "With so many researchers dissecting so many genomes now, it's reasonable to suggest that there might be more waiting to be found.
"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 research was supported by the National Science Foundation, the National Institutes of Health, the Department of Energy and the Alfred P. Sloan Foundation. Along with Krzycki, Chan and Hao, Weimin Gong and Tsuneo Ferguson worked on the project.
Dick. Here have some more powerery crap that will make your balls shrink. I think that it will make a muscle fiber too. Don't eat any food!
The only time or place for farting is while cracking one on the toilet!
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.
Here is a mirror.
Alan Thicke's Journal
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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 is a good page for more info on codons, their product amino acids and more.
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.
This is my sig. The post is over.
Ah! Here's the original article: Code Breakers. It's definitely worth a read.
Steven N. Severinghaus
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.
"It is a greater offense to steal men's labor, than their clothes"
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? :)
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.
"Never, never suspect the dreams within the dreams of dreaming children." ~The Amazon Quartet
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.
"Never, never suspect the dreams within the dreams of dreaming children." ~The Amazon Quartet
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 and has been extensively researched at Howard Hughes Medical Center. Naturally the Japanese have established a whole new research center on this at SRUT (Japanese character module required) so can a special edition of Iron Chef be far behind?
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.
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?
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.)
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.
Don't worry, you will have a friend called Arthur Dent ;)
* Origin: XBase BBS (2:490/4100) Well the good old days may not return and rocks might melt and sea may burn.
Sure they provide 'all' the essential amino acids your body cannot produce or produce in large enough quantities... but it doesn't stop there. The mineral and vitamin requirements are often ignored by those who only look into protein. Supliments are not the best thing, but are better than doing without. Perhaps our bodies work they way they do and we should accept that and make due the best we can. Illogical rhetoric does not provide me with skeletal stability. Emotional ramblings do not provide me with energy, minus dangerous amounts of toxic biproducts that kidneys and livers cannot keep up filter wise.
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.
[snip] Dried bull's spunk?
Seriously though, is slashdot now getting people creating accounts just to plug products, or was this just a coincidence (I suppose geeks get employment from all sorts of companies)?
Be careful! New moon tonight.
Sounds like you had a lot to get off your chest... that was quite an impressive rant. Incidentally, by what logic do you begin ranting against processed foods in reply to a sentence that mentioned rice and beans?
Win dain a lotica, en vai tu ri silota
Actually I was interested in knowing which is/are the mRNA three-letter code for this new aminoacid. Could not find it in the link. Any ideas?
This is one of the few posts that has got it right.
There are in fact something like 80 naturally occurring amino acids. Many of us were taught that 20 are "found in proteins". What this really means is that there are 20 which are incorporated into proteins using the translational machinery (they have a tRNA, a corresponding DNA codon and are processed at the ribosome). Furthermore these amino acids are all L-amino acids.
Next, post translational modifications were discovered, meaning that the amino acids may be chemically altered, but after they have been inserted into the protein chain. This includes things like hydroxyproline, in collagen.
A few years ago, we discovered selenocysteine, which is only cysteine with a bound Se. But it is incorporated using translation, using a tRNA and a codon that would normally be a "stop" signal (an amber codon).
So now we have pyrrolysine. A very interesting discovery, properly termed "the 22nd amino acid that is incorporated into proteins using the standard translational machinery".
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.
This is my sig. The post is over.
I was wondering. How do they know that it is called pyrrolysine? I mean - it ends in lysine - which makes for a good aminoacid name but still...
virve
--
just a thought
BOFH_org
PLEASE PASS THE MILK PLEASE
PLEASE PASS THE MILK PLEASE
PLEASE PASS THE MILK PLEASE
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(Crap added to avoid the lameness filter)
Processed foods, powdered sugars, flour, etc
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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.
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