Chemical bonds

The things one can do with light - and messages in the dark

jhalper — Tue, 01 Sep 2015 02:56:50 +0000

The things one can do with light - and messages in the dark

One day in the future, we may be treating our ailments with microbiotic combinations designed specifically to correct imbalances in our personal microbiomes. We’ll bring our prescriptions on rewritable paper and pay using shimmery optical chips embedded in our cell phone cases or maybe our jewelry. Or we’ll be waiting in our doctor’s office for a simple test of our microbiogenome to see if a light-based nanoparticle delivery treatment is working, while watching iridescent optical displays that change as we move...

These future scenarios (and many more) are all imaginary, but they are imminently feasible, given today’s new stories on basic research at the Weizmann Institute. These are about several things one can do with light, including a disappearing trick or two, and messages hidden in deep, dark places.

Dr. Rafal Klajn’s messages are written with light. Printed images on a unique surface disappear within a few minutes. This system, made of nanoparticles in a gel-like medium, can be rewritten over and over again, so it could, one day, be the basis of rewritable paper. Klajn’s innovation is to put light-sensitive molecules into the medium (rather than engineering the nanoparticles); light exposure turns the gel acidic and leads to a fairly simple chemical reaction with the nanoparticles that causes them to disperse. The molecules Klajn uses, by the way, were developed back in the day (1950s) at the Weizmann Institute, and they have been used, among other things for photosensitive coatings on glasses.

Lighting the medium causes nanoparticles to disperse. Image: lab of Dr. Rafal Klajn

A different trick of the light is that of a tiny marine creature commonly known as a sea sapphire. Only a millimeter or so in length, the males of several species flash in brilliant colors ranging from purple to green for a second or so, and in the next they appear to completely vanish from sight. Though we still don’t know if the colors are meant to attract females or warn other males, thanks to Profs. Lia Addadi, Steve Weiner and Dan Oron, and their students Dvir Gur and Ben Leshem, we now know exactly how they perform the trick. Thin, clear crystals on the sea sapphires’ backs are stacked in precise arrays with “spacers” of cellular material holding them in place. It is the tuning of the spaces between the crystals that cause light to be directed in very specific wavelengths. In some species, this creates a glitzy blue iridescence when the light hits them full-on, from above. But when the sea sapphire performs an evasive corkscrew maneuver in the water, the angles are foreshortened as it turns sideways and the reflected light is shifted into the ultraviolet – effectively creating a sort of temporary invisibility cloak.

The precise stacking of the crystals, say the researchers, could lead to the design of artificial nanophotonic structures that would have numerous applications.

[embed]https://youtu.be/26kus22RaTo[/embed]

Finally, a study that brings to light a signal hidden in a place that daylight never reaches – deep inside our intestinal tracts. We know by now that the thousands of different types of bacteria living there are writing their own messages, which our immune systems interpret to our benefit or detriment. Type 2 diabetes, for example, and inflammatory bowel disease are mediated by the mix of microorganisms in our guts. Today we can work out the makeup of a person’s gut microbiome, but its message is mostly still too faint to read.

Computer scientist Prof. Eran Segal and his research students, working together with the group of Dr. Eran Elinav, an immunologist, have come up with a way of identifying a sort of communiqué within the broad picture. The idea is to sequence all of the DNA in a single sample, a task that is already available today with advanced sequencing techniques. Such techniques break the DNA into pieces and then reassemble the short sequences into long ones. But the group showed that this information can tell you not just quantities each kind of bacterium, but how fast each is reproducing. That’s because many of them are in the process of copying out their genomes in preparation for splitting into daughter cells; thus an overall sequencing will turn up lots of partial genomes. Since each kind of bacterium conveniently starts copying at the same point in its circular genome, one can figure out the first and last sequences to be copied and compute the ratio between the two. That will tell you, from a single sample, how fast each is replicating.

And changes in growth rates, according to the team’s further analysis, is a better indicator of the above-mentioned disorders than any other attempt to read our microbiomic messages, so far.

Three different studies – all basic research – in departments ranging from physics to computer science to chemistry and biology. The future possibilities are endless.

jhalper Mon, 08/31/2015 - 22:56

Tags

autoimmune disease

basic research

Biological networks

Biomedical

Chemical bonds

Chemical communication

personalized medicine

inflammatory syndrome

There Once Was A....

jhalper — Mon, 11 Aug 2014 03:31:10 +0000

There Once Was A....

Once again, there are three new pieces online on our website, each wonderful in its own way. But Haiku just didn’t seem to fit this batch. So, with apologies to the scientists, here are three limericks on the newest Institute research. As before, follow the links to get to our website.

(Incidentally, there is some precedent for limerick writing at the Weizmann Institute. The late Prof. Amikam Aharoni, who also wrote some serious stuff on ferromagnetism, was known for his limericks.)

The Quasar

There once was a baby black hole

That went for a short little stroll

It zigged and it zagged

Appetite never lagged

Til it’d swallowed its neighborhood whole

Nanostrings Attached

To make a string out of cubes

Don’t reach for those long nanotubes

To twist like a screw

Only one shape will do

Those nano-self-assembling cubes

The Stem Cell’s Story

What, oh what, will I be tonight?

A red blood cell, or maybe a white?

Though I’m bound for the red

I’ll stop just ahead

And turn into a nice lymphocyte

jhalper Sun, 08/10/2014 - 23:31

Tags

What Do Your RiboSNitches Tell about You?

jhalper — Thu, 15 May 2014 04:48:44 +0000

What Do Your RiboSNitches Tell about You?

At the level of biomolecules, life boils down to two basic principles: sequence and folding. We know, for example, that the sequence of nucleotides in the DNA contains our genetic blueprint, but the way that our DNA is folded and wrapped up in each chromosome helps determine which genes are easily accessible for copying. Proteins – sequences of amino acids – fold into intricate shapes before assuming their duties. So it is no surprise that the third main molecular sequence in the cell – the RNA, made up of single strands of nucleotides – folds as well. Nucleotides are built to pair up – DNA to its matching strand in the genome, DNA to RNA for copying, RNA to the small RNAs that effect translation to protein. And when it is on its own, that tendency to pair up causes the RNA strand to fold over on itself.

The unique, hairpin curves and bulges in the RNA strands owe their shapes to the fact that certain pairs of nucleotides are more strongly attracted than others. So you could be forgiven for thinking the shape of a folded RNA molecule is a chance artifact of the DNA code. Indeed, the overwhelming mass of research on RNA focuses on its sequence and ignores its shape.

RiboSnitches: these RNA segments in the mother and father have slightly different sequences, but very different folding patterns

Hence the results of a recent study conducted at the Weizmann Institute and Stanford that mapped the folded landscape of RNA were something of a surprise: They revealed a distinct logic, unique to the RNA, in its curves and loops. When the map – constructed from an analysis of nucleotide pairing from hundreds of millions of RNA fragments – was laid out, its formations suggested a legend and key. Certain larger loops appear to mark spots where activity should take place, for example, starting or stopping protein production. The researchers even noted bumps every three nucleotides that could delineate codons – sequences encoding a single amino acid.

In other words, in an evolutionary twist on the idea that the sequence dictates folding and form, here the folds appear to enhance the sequence, adding “notes” that may possibly help the protein manufacturing machinery decipher the code more efficiently.

How important are those notes? Scientists will have to conduct further research to answer that question. But Prof. Eran Segal, the Weizmann researcher involved in creating the map, thinks they might play a role in key biological processes and diseases. In comparing the folds from three different individuals – two parents and a child – they noted that in around 15% of the regions with SNPs – where the parents’ DNA varied by a single nucleotide – the folding shapes were affected, sometimes significantly. The scientists gave these variations in the RNA landscape the endearing name “RiboSNitches,” and proceeded to locate them on the map. Eventually, they think, these RiboSNitches could become real “snitches” – symbols on the RNA maps that can point to possible misreading of the coded sequence.

jhalper Thu, 05/15/2014 - 00:48

Tags

RNA folding landscape

single nucleotide

basic research

Nutrient-dependent / Pheromone–controlled thermodynamics and thermoregulation
file:///C:/Users/Guest/Downloads/Nutrient_dependent_Pheromone_controlled_Thermodynamics_and_Thermoregulation.pdf

5.5 minute video from ISHE Summer Institute 2013
http://www.youtube.com/watch?v=DbH_Rj9U524

Guest Post: Astrochemistry and how the Universe comes together

esiegel — Thu, 01 Aug 2013 09:41:27 +0000

Guest Post: Astrochemistry and how the Universe comes together

“We are not simply in the universe, we are part of it. We are born from it.” -Neil deGrasse Tyson

The story of the Universe is the story of us all; we all share the same cosmic history, coming from a hot, dense state some 13.8 billion years ago known as the Big Bang and emerging after billions of years of cosmic evolution to the Universe we know and love today.

Image credit: ESA and the Planck collaboration.

It's a beautiful story -- and one I've told before -- but it might seem, at least from our perspective, that something is missing from the astrophysicist's version of events. Yes, we can start with a hot, dense, expanding Universe full of matter, antimatter and radiation, create some asymmetry between matter and antimatter, and then have the Universe expand and cool. Below a certain temperature, the antimatter will annihilate away with the vast majority of the matter, leaving only the tiny, asymmetric amount of matter (less than 1-part-in-a-billion) bathed in a sea of radiation.

Image credit: me, background by Christoph Schaefer.

But this radiation is constantly dropping in temperature as the Universe expands, having its wavelength stretched by the expansion of space. At some point, the Universe becomes cool enough that two types of matter particles you know -- protons and neutrons -- can fuse together without being immediately blasted apart by this sea of radiation.

Images taken from LBL, stitched together by me.

These nuclear fusion reactions give it all they've got, but by time this can happen, it's very difficult to get densities (or energies) high enough to form very heavy elements. During the first few minutes after the Big Bang, we can create a substantial amount of helium in the Universe, and tiny, trace amounts of Lithium and Beryllium, but that's it. The story of Big Bang Nucleosynthesis is amazing, but it doesn't tell us where we come from.

Image credit: Ned Wright's cosmology tutorial; data from Burles, Nollett & Turner (1999).

By number, it gives us a Universe which is 92% hydrogen, 8% helium, and less than 0.0000001% everything else combined. In fact, if we want the elements we consider essential to life -- Carbon, Nitrogen, Oxygen, Phosphorous, etc. -- we have to look well past the early stages of the Universe, and fast-forward to the formation of stars!

Image credit: NASA/JPL-Caltech/L. Allen and the IRAC GTO Team.

The more massive your star is, the heavier the element it's capable of fusing together. Also, the more massive your star is, the faster it burns through its fuel! A star like our Sun will fuse helium into carbon, nitrogen, and oxygen, while a substantially more massive star like Sirius (the brightest in our sky) will fuse those elements further into silicon, sulphur, and all the way up to iron, nickel and cobalt. When these stars run out of fuel, they'll return a fraction of these heavy elements back into the cosmos when they expel a large fraction of their mass into a planetary nebula.

Image credit: Vicent Peris, José Luis Lamadrid, Jack Harvey, Steve Mazlin, Ana Guijarro.

But the elements heavier than that -- as well as the vast majority of all elements heavier than helium -- come from the catastrophic deaths of the most massive stars: the one that die in core-collapse supernovae! Whenever a star more than about 8-to-10 times the mass of the Sun is formed, it burns through all of its nuclear fuel in just a couple of million years, maximum, and its core collapses down to a neutron star or black hole, destroying the rest of the star. Large amounts of the first 28 elements of the periodic table are recycled back into the Universe, where they can form the next generation of planets and stars.

Image credit: ESO / Very Large Telescope / FORS instrument & team.

But a huge number of free neutrons are also created, and through two creatively named processes -- the rapid r-process in the supernova itself and the slow s-process in the later stages of these stars' lives -- the heavier nuclei are created, including everything up-to-and-including Plutonium, and probably even beyond!

Image credit: wikipedia user 28bytes, under CC-BY-SA-3.0.

Yes, these elements will continue on in the next generation of stars, planets, and whatever else happens to come to exist in the Universe, making up as much as 1% of the Universe by mass (although much less than that by number). But there's a long way to go from atomic nuclei to the world we know today. And that connection goes far beyond my expertise. Luckily, I've got a very smart friend whose expertise lies in chemistry (and who has guest blogged for us before), and he's agree to take us through some of the basics of astrochemistry, or how these elements bind together to form molecules in the Universe. [My comments in square brackets.] Take it away, Richard Helmich!

Thanks Ethan for the excellent lead in and introduction. From the many generations of stars, the Universe has generated plenty of elements, and humans have even taken their time to organize them into the periodic table. These are very same elements found in you and me, and out in space these atoms don’t simply float around and do nothing. They react with each other to form all kinds of familiar and exotic molecules. Let’s take a look at what chemicals we’ve found outside of Earth so far…

Image credit: Wikimedia Commons users Cepheus and DePiep.

Hang on a minute… what are astrochemists looking for, exactly? Similar to how atoms absorb and emit light characteristic to a particular element in planetary nebulae like the Ring Nebula, whole molecules can absorb energy and emit light of particular frequencies characteristic to that molecule.

Image credit: NASA, ESA, C.R. O'Dell (Vanderbilt), and D. Thompson (Large Binocular Telescope).

The wavelength of light that a molecule absorbs or emits depends on what the atoms in the molecule are doing before and after the light is absorbed or emitted. The atoms in the molecule can vibrate in relation to each other in various ways, or the whole molecule can start or stop spinning as a whole.

Symmetrical stretching	Asymmetrical stretching	Scissoring

Rocking	Wagging	Twisting

The study of the energy atoms and molecules absorb and emit is an entire field of science called spectroscopy. Scientists have been able to discover the identities (and sometimes even the concentrations) of molecules that form throughout the universe by using spectroscopy to examine the infrared and millimeter wavelength light emitted by molecules in outer space. The amount of light given off at these wavelengths is typically very small, but fortunately scientists have been able to build very powerful telescopes such as the Herschel Space Observatory, Spitzer Space Telescope and -- here on Earth -- the Atacama Large Millimeter/Sub-millimeter Array (ALMA) to investigate astrochemistry in the nearer parts of the universe.

Image credit: ALMA (ESO/NAOJ/NRAO) (main); Herschel Space Observatory / ESA (inset).

So what have scientists found out in the vast expanses of space so far?

LOTS!

Here are just a few that have been identified, that are also common on Earth. (And there's a more complete list here.)

A few molecules found in outer space.

2 atoms

Carbon Monoxide

NaCl

Sodium Chloride

Nitrogen Monoxide

Carbon Monosulfide

3 atoms

H₂O

Water

HCN

Hydrogen Cyanide

H₂S

Hydrogen Sulfide

FeCN⁺

Iron (II) Cyanide

4 atoms

C₂H₂
Acetylene

NH₃

Ammonia

H₂CO

Formaldehyde

H₂O₂

Hydrogen Peroxide

Others

CH₃OH

Methanol

SiH₄

Silane

CH₃CHO
Acetaldehyde

C₆₀

Buckminsterfullerene

So let’s follow what happens to the elements created as a star dies and then are recycled again into a new star…our first stop is IRC +10216.

Image credit: Izan Leao (Universidade Federal do Rio Grande do Norte, Brazil).

This star was once between 3 and 5 times the mass of our sun, Sol. This star is in the late stages of becoming a white dwarf, and is in the process of blowing off its outer most layers into interstellar space. An astute scientist studying this star noticed it had a plethora of chemicals and was even able to map the location of some of them.^[1]

Image credit: from Dayal and Bieging, 1993; an older study of this star.

This map is awesome! Some scientists are figuring out various ways to do this for very small objects located on Earth, while others have mapped the molecular makeup of a star hundreds of light years away. [This star, in particular, is some 400 light-years distant from Earth.] This map has given scientists insight into the evolution of this star during its dying moments.

This is a molecular map of the vicinity surrounding IRC+10216 showing the locations of some molecules observed. From reference 1.

The NaCl (the same as the salt you have in your kitchen, minus the added iodine) is only observed near the core where temperatures are hot enough to keep it in the gas phase. Farther away there is likely to still be NaCl, but it has cooled and condensed into dust and is no longer obserable. Magnesium isocyanide, MgNC, is another metal salt like NaCl. This molecule is peculiar because on Earth the magnesium atom would be bound to the carbon (MgCN), but the reaction in outer space is kinetically driven (molecules and atoms bumping into each other) not thermodynamically determined so typically the abundance of each isomer is approximately equal.^[2] Other molecules were also observed such as HC₅N and C₄H. These are acetylenic molecules (similar to acetylene used in welding torches) with alternating single and triple bonds between the carbons atoms.

Later, after the star has proceeded further along its path towards becoming a white dwarf, the amount of UV light it emits increases, forming a planetary nebula when the gases become ionized. The UV light given off by the newly formed white dwarf typically causes much of the previously formed gaseous molecules to decompose, but recently scientists have observed that some molecules are still able to hold together.

Image credit: WFI, MPG/ESO 2.2-m Telescope, La Silla Obs., ESO (L). Concentration of CO (top right) and emission lines for the acetylene radical (bottom right) where the CO signal is strongest; via reference 1.

Moving from the death of stars to the birth of the next generation of stars, other scientists have observed the chemicals present in molecular clouds as they condense and form new stars. Scientists have observed water, carbon dioxide, silicates (similar to the grains of sand found on any beach), and even polyaromatic hydocarbons (also found in crude oil).^[3]

Image credit: ESO, HAWK-1 Instrument Team (top); spectra indicating various chemical compounds via reference 3 (bottom).

This group of scientists observed the molecular fingerprints of many newly forming stars before stumbling on protostar IRS46 in Ophiuchus. The protostar showed a very interesting mix of acetylene (C₂H₂), hydrogen cyanide (HCN), and carbon dioxide (CO₂) gases.

Images credit: via reference 3, below.

None of the other protostars observed had these gases, possibly because IRS46 is oriented with it’s planet forming plane directly along Earth’s line of sight. Observing these gases around protostars is very exciting, because they are some of the most basic building blocks of protein and DNA! [Other protostars, such as HH46 IRS, offer some spectacular absorption features of some common molecules as well in their outflows.]

Image credit: Noriega-Crespo et al. 2004, ApJS, 154, 352.

So there you have it, a taste of astrochemistry! Our universe is full of fantastic stars that are fusing heavier elements from the hydrogen and helium created during the Big Bang and recycling them into supernovae and planetary nebulae, more stars, planets, and even you and me. When you look up into the night sky now, I hope you’ll keep in mind that while there’s a lot of hydrogen floating around out there, there’s also much, much more.

BONUS: “BUT WAIT! How do these reactions happen when the universe is generally so COLD?!”

Good Question! Some scientists recently suggested quantum tunneling might be the answer.^[4] If you get a smirky ‘cool’ smile anytime quantum tunneling is mentioned, don’t worry, I do too. Let me take a second to explain more clearly what quantum tunneling is, exactly. Quantum tunneling is a process where a very small portion of many particles are able to tunnel through an insurmountable energy barrier instead of traveling up and over the energy barrier. So what does quantum tunneling have to do with chemistry in interstellar space? Well, every chemical reaction has some energy barrier between the reactants and products. This energy barrier is called the activation energy of the reaction. Sometimes the thermal energy at room temperature is enough of a kick for a reaction (acid-base reactions), while other reactions require a much harder push (a spark to ignite the gas in your car’s engine).

Image credit: Richard Helmich.

Back to astrochemistry, among the more common molecules found in the universe are methanol (CH₃OH) and hydroxyl radicals (·OH). These chemicals react to create a methoxy radical (CH₃O·) and water. All of these have been observed in outer space, but the activation energy required for this reaction was thought to effectively prevent it from happening at the temperatures found in outer space, ~ 20 K. No one had actually attempted to measure how well these chemical reacted with each other at temperatures approximating those in space. Until now!

Image credit: Arrhenius plot of the reaction rate constant, k1, verses temperature for CH3OH + -OH ↔ CH3O+ + H2O. Via reference 4.

This graph shows the reaction rate constant for methanol reacting with hydroxyl radicals. Data on the left are historical and show the thermodynamic reaction path. As the temperature decreases, the rate of the reaction also decreases, but those two points on the upper right (2σ-shown) show that at even lower temperatures, the rate increases. One of the ways for a chemical reaction to form products faster than the thermodynamic path (and the most likely culprit for this reaction) is for quantum tunneling to occur. The solid line is the combined thermodynamic and quantum tunneling best fit computer model.

The Universe is an amazing place to live, and nature always finds a way to do what it wants. Even if that means a little cheating via quantum tunneling. ☺

References:

Ziurys, Lucy M. The chemistry in circumstellar envelopes of evolved stars: Following the origin of the elements to the origin of life Proceedings of the National Academy of Sciences2006, 103, 12274-12279.
Klemperer, William Interstellar Chemistry Proceedings of the National Academy of Sciences of the United States of America 2006, 103, 12232-12234.
Dishoeck, Ewine F. Chemistry in low-mass protostellar and protoplanetary regions Proceedings of the National Academy of Sciences 2006, 103, 12249-12256.
Shannon, Robin J.; Blitz, Mark A.; Goddard, Andrew; Heard, Dwayne E. Accelerated chemistry in the reaction between the hydroxyl radical and methanol at interstellar temperatures facilitated by tunnelling Nat Chem, advance online publication.

esiegel Thu, 08/01/2013 - 05:41

Tags

Thanks so much for the guest post. That was awesome.

Thank you Richard and Ethan

I hope this isn't too off topic... In the period just before the formation of the first suns [380M years after BB] could there have been all the elements present, but in absolutely minute quantities for those above Be-8? I'm thinking that there must have been instances of fortuitous collisions between atoms where the energies were sufficient to form minuscule amounts of the elements B, C, N, O etc without processing through stars

Just a thought...

Michael,

According to my calculations, Beryllium-9 is a pretty hard limit. The Coulomb barrier becomes very large and the Universe is pretty cold by time Helium forms, so while it's conceivable that you might get lucky and wind up with a few atoms of Boron, I don't see how Carbon-and-higher will be formed. That is to say, there are only around 10^80 atoms in the observable Universe, and the odds of forming Carbon (or higher) during Big Bang Nucleosynthesis is somewhere in the vicinity of less than 10^-80, probabilistically.

The universe would have more atoms in it before inflation took them away, Ethan.

Though that would have to be a hell of a lot more to get *Carbon* forming, since the energies aren't appropriate until you add a million degrees of heat in the atmosphere of a large sun to make up the difference.

But it could give a chance of an over-production of Helium making Carbon possible.

Hyper-stars would be an easier option and may be the only (if extremely rare) type of star that could form that early in the universe.

A prof at my university has some pet theories about that, never took it far enough to put limits on the options made possible, though.

Maths beyond ten fingers is hard... :-)

Very interesting post. I find it mind-blowing that detailed knowledge of the chemical constituents of such remote astrophysical bodies can be gleaned from astronomical instruments. To find evidence of the molecules that make up building blocks of proteins and DNA, already formed around nascent stars -- that's stupendous stuff. Part of me feels that people should be shouting this stuff in the streets -- but my family would dismiss that as the geek within me talking. Keep up the good work on this excellent blog.

Really awesome post !!! a taste of real chemistry behind dark science.

A very fascinating book giving the history (and physics) of these discoveries is one by Marcus Chown entitled "The Magic Furnace (The search for the origin of Atoms)"

"a taste of real chemistry behind dark science."

If you want a real "taste" of chemistry, how about this: The center of the milky way tastes like raspberries and smells of rum! Think I'm lying? Look it up!

I've seen reports recently on how neutron star collisions, as a hypothetical source of short-duration gamma ray bursts, may be responsible for quite a bit of the synthesis of "neutron rich" heavy elements (e.g. gold). How significant this is compared to say "standard(?)" nucleosynthesis via supernovae?

http://arstechnica.com/science/2013/07/making-heavy-elements-by-collidi…

love your site .

Getting into the Fray

jhalper — Mon, 22 Oct 2012 06:12:08 +0000

Getting into the Fray

“The public, blog-fueled controversy over the utilization of arsenate instead of phosphate in bacteria was, in the end, a demonstration of what is truly right with scientific quests,” says Prof. Dan Tawfik. “The original findings (that certain bacteria can use arsenate instead of phosphate) may have been overhyped. The research itself may have been underwhelming. But what ensued is exactly what should have happened: The correcting mechanisms that are intrinsic to science kicked in. Other experimental groups examined the claims in their labs and found them to be unsupported. And new scientific questions arose in their wake. All in all, some very good science came out of those questionable findings.”

Tawfik and postdoc Dr. Mikael Elias should know. Their recent study might settle the arsenate debate once and for all. But their work also turns out to be a powerful demonstration of evolutionary fine-tuning in proteins that function in an inhospitable environment.

On the face of it, the original claim was convincingly put: The bacteria in question live in lake sediment with a high arsenate content. Since arsenate is chemically nearly identical to phosphate, it might almost stand to reason that these microorganisms have evolved to substitute the normally toxic substance for the phosphate that all known life forms use to build DNA and other vital metabolic compounds. But, say Tawfik and Elias, phosphate's unique chemical properties are so basic to life that such bacteria would pretty much have to reinvent biochemistry (Others have since shown that these bacteria do, indeed, rely on phosphate, alone.)

Once and for all: No arsenate uptake. Image: NASA

And yet, a niggling question remained: How do the bacterial proteins responsible for taking up phosphate from the environment manage to select the desired molecule and avoid picking up the toxic arsenate instead? Tawfik and Elias had their first clue when they compared the function of this protein in several different bacterial species – some that routinely live with arsenate and others that don’t. It turns out that the phosphate import machinery of all bacteria they tested is pretty good at selecting phosphate over arsenate. But those that make their home in arsenate-filled sediments are really proficient: The chances that they’ll accidentally pick up an arsenate molecule are less than one in 5000. So, instead of adapting by making use of the environmental arsenate, these bacteria have actually evolved to reject it ever more efficiently.

Further research (including a crystallization technique that enabled the researchers to resolve the atomic structure of the protein bound to a phosphate or arsenate molecule down to single hydrogen atoms) revealed how the bacterial import protein selects phosphate. It all comes down to the angle of an unusually short and energetic bond between a certain hydrogen atom in the protein and the bound molecule. This atom is a sort of “phosphate checker”: When the slightly larger arsenate molecule binds, it squeezes up against the protein at some very unfavorable angles. This turns out to be cause for arsenate rejection.

Tawfik and Elias also point out that understanding this clever selection mechanism may have implications for other areas, for instance agriculture, in which the efficient uptake of phosphate is often crucial. All thanks to a scientific storm. Tawfik: “Heated controversy, getting into the fray, is not a bad thing in science. The eminent Max Perutz made this point in his essay I Wish I Had Made You Angry Earlier. If it weren’t for the scientific debate, we might never have stumbled on the question, much less found the answer.”

jhalper Mon, 10/22/2012 - 02:12

Tags

biochemistry

Biophysics

Chemical bonds

Proteins in living cells

All is fine with that if you have the right friends, nonsense goes into high IF journals? It is good science that criticism has to go through internet viral mechanisms, here perhaps both times partially because a women researcher was involved and could be exploited to make a political point, all that is fine? What a corruption of science! What about the memristor scandal, where the same happened, namely nonsense going into those super high IF journals:
www.science20.com/alpha_meme/memristor_another_science_scandal-92795
Oh - right - you did not hear about it, precisely because of those "fine" mechanisms. Well played everybody - no wonder the public does no longer trust science!

Actually, you only have to look at this blog or through our website to see excellent science by women. (See the previous 2 out of 3 posts.) Do you think that women should somehow be above the scientific fray?

I think that the main reason the arsenate findings were overhyped is that arsenic has a certain hold on the popular imagination. Had the bacteria been thought to have the ability to metabolize antimony, no one outside the field would have heard been aware of the claim.

Yes, it would have been quite cool if it were true, and there would have been implications for astrobiology, as well, which is apparently why NASA rushed to publicize it.