Tag Archives: biochemistry

BigBang

A Painful End

This should come as no surprise — advances to our understanding of biochemical and genetic processes seem to make the news with ever-increasing regularity. Researchers seem to have found the mechanism for switching physical pain on and off in mammals. They recently succeeded in blocking and restoring pain signals in mice. And, through the same discovery have been able to restore the sensation in a woman who has an extremely rare condition that makes her unable to feel any pain. It’s all in the Nav1.7 sodium ion channel and in its regulation of opioid peptides.

Fascinating, but where will this lead us? And, more to the point, will there ever be a pill to end the interminable pain of the US political process?

From ars technica:

Physical pain is a near universal problem, whether its sudden pangs or chronic aches. Yet, researchers’ efforts to quash it completely have fallen short—possibly due to a moonlighting channel in nerve cells. But that may be about to change.

The sodium ion channel, called Nav1.7, helps generate the electrical signals that surge through pain-related nerve cells. It’s known to play a key role in pain, but researchers’ past attempts to power-down its charged activities did little to soothe suffering. In a bit of a shocking twist, researchers figured out why; the channel has a second, un-channel-like function—regulating painkilling molecules called opioid peptides. That revelation, published in Nature Communications, provided researchers with the know-how to reverse painlessness in a woman with a rare condition, plus make mice completely pain free.

The link between Nav1.7 and opioid painkillers is “fascinating,” Claire Gaveriaux-Ruff, a pain researcher and professor at the University of Strasbourg, told Ars. And, she added, “this discovery brings hope to the many patients suffering from pain that are not yet adequately treated with the available pain medications.”

That source of hope has been a long time coming, John N. Wood, lead author of the study and a neuroscientist at University College London, told Ars. Researchers have been interested in Nav1.7 for years, he said. Excitement peaked in 2006 when scientists reported finding a family who lacked the channel and could feel no pain at all. After that, researchers excitedly scrambled to relieve pain with Nav1.7-blocking drugs. But the drugs inexplicably failed, Wood said. “So we thought, well maybe this channel isn’t just a channel, maybe it’s got some other activities as well.”

Using genetically engineered mice, Wood and colleagues found that completely shutting off Nav1.7 not only made mice pain-free, it cranked up their amount of opioid peptides in nerve cells. These molecules are natural painkillers that help the body moderate pain responses. In these Nav1.7-lacking mice, opioid levels were extremely high, blunting all twinges and throbs. When the researchers gave the mice a drug that blocks those opioids, the animals could feel pain normally. (The opioid-blocking drug, naloxone, treats overdoses of opioid drugs, such as morphine and codeine.)

Even more promising, Wood and colleagues saw the same result in a person. The test subject, a 39-year-old woman with a rare mutation that shuts off Nav1.7, had been pain-free all her life. But, when the researchers gave her a dose of the opioid-blocking naloxone, she felt pain for the first time—the sting of a tiny laser. She was happy to go back to her normal, painless state after the drug wore off, Wood reported. But, she hopes that the drug treatment can be used in children with the pain-free condition to keep them from unknowingly injuring themselves.

Read the entire article here.

BigBang

Metabolism Without Life

Glycolysis2-pathway

A remarkable chance discovery in a Cambridge University research lab shows that a number of life-sustaining metabolic processes can occur spontaneously and outside of living cells. This opens a rich, new vein of theories and approaches to studying the origin of life.

From the New Scientist:

Metabolic processes that underpin life on Earth have arisen spontaneously outside of cells. The serendipitous finding that metabolism – the cascade of reactions in all cells that provides them with the raw materials they need to survive – can happen in such simple conditions provides fresh insights into how the first life formed. It also suggests that the complex processes needed for life may have surprisingly humble origins.

“People have said that these pathways look so complex they couldn’t form by environmental chemistry alone,” says Markus Ralser at the University of Cambridge who supervised the research.

But his findings suggest that many of these reactions could have occurred spontaneously in Earth’s early oceans, catalysed by metal ions rather than the enzymes that drive them in cells today.

The origin of metabolism is a major gap in our understanding of the emergence of life. “If you look at many different organisms from around the world, this network of reactions always looks very similar, suggesting that it must have come into place very early on in evolution, but no one knew precisely when or how,” says Ralser.

Happy accident

One theory is that RNA was the first building block of life because it helps to produce the enzymes that could catalyse complex sequences of reactions. Another possibility is that metabolism came first; perhaps even generating the molecules needed to make RNA, and that cells later incorporated these processes – but there was little evidence to support this.

“This is the first experiment showing that it is possible to create metabolic networks in the absence of RNA,” Ralser says.

Remarkably, the discovery was an accident, stumbled on during routine quality control testing of the medium used to culture cells at Ralser’s laboratory. As a shortcut, one of his students decided to run unused media through a mass spectrometer, which spotted a signal for pyruvate – an end product of a metabolic pathway called glycolysis.

To test whether the same processes could have helped spark life on Earth, they approached colleagues in the Earth sciences department who had been working on reconstructing the chemistry of the Archean Ocean, which covered the planet almost 4 billion years ago. This was an oxygen-free world, predating photosynthesis, when the waters were rich in iron, as well as other metals and phosphate. All these substances could potentially facilitate chemical reactions like the ones seen in modern cells.

Metabolic backbone

Ralser’s team took early ocean solutions and added substances known to be starting points for modern metabolic pathways, before heating the samples to between 50 ?C and 70 ?C – the sort of temperatures you might have found near a hydrothermal vent – for 5 hours. Ralser then analysed the solutions to see what molecules were present.

“In the beginning we had hoped to find one reaction or two maybe, but the results were amazing,” says Ralser. “We could reconstruct two metabolic pathways almost entirely.”

The pathways they detected were glycolysis and the pentose phosphate pathway, “reactions that form the core metabolic backbone of every living cell,” Ralser adds. Together these pathways produce some of the most important materials in modern cells, including ATP – the molecule cells use to drive their machinery, the sugars that form DNA and RNA, and the molecules needed to make fats and proteins.

If these metabolic pathways were occurring in the early oceans, then the first cells could have enveloped them as they developed membranes.

In all, 29 metabolism-like chemical reactions were spotted, seemingly catalysed by iron and other metals that would have been found in early ocean sediments. The metabolic pathways aren’t identical to modern ones; some of the chemicals made by intermediate steps weren’t detected. However, “if you compare them side by side it is the same structure and many of the same molecules are formed,” Ralser says. These pathways could have been refined and improved once enzymes evolved within cells.

Read the entire article here.

Image: Glycolysis metabolic pathway. Courtesy of Wikipedia.

BigBang

From RNA Chemistry to Cell Biology

Each day we inch towards a better scientific understanding of how life is thought to have begun on our planet. Over the last decade researchers have shown how molecules like the nucleotides that make up complex chains of RNA (ribonucleic acid) and DNA (deoxyribonucleic acid) may have formed in the primaeval chemical soup of the early Earth. But it’s altogether a much greater leap to get from RNA (or DNA) to even a simple biological cell. Some recent work sheds more light and suggests that the chemical to biological chasm between long-strands of RNA and a complex cell may not be as wide to cross as once thought.

From ars technica:

Origin of life researchers have made impressive progress in recent years, showing that simple chemicals can combine to make nucleotides, the building blocks of DNA and RNA. Given the right conditions, these nucleotides can combine into ever-longer stretches of RNA. A lot of work has demonstrated that RNAs can perform all sorts of interesting chemistry, specifically binding other molecules and catalyzing reactions.

So the case for life getting its start in an RNA world has gotten very strong in the past decade, but the difference between a collection of interesting RNAs and anything like a primitive cell—surrounded by membranes, filled with both RNA and proteins, and running a simple metabolism—remains a very wide chasm. Or so it seems. A set of papers that came out in the past several days suggest that the chasm might not be as large as we’d tend to think.

Ironing out metabolism

A lot of the basic chemistry that drives the cell is based on electron transport, typically involving proteins that contain an iron atom. These reactions not only create some of the basic chemicals that are necessary for life, they’re also essential to powering the cell. Both photosynthesis and the breakdown of sugars involve the transfer of electrons to and from proteins that contain an iron atom.

DNA and RNA tend to have nothing to do with iron, interacting with magnesium instead. But some researchers at Georgia Tech have considered that fact a historical accident. Since photosynthesis put so much oxygen into the atmosphere, most of the iron has been oxidized into a state where it’s not soluble in water. If you go back to before photosynthesis was around, the oceans were filled with dissolved iron. Previously, the group had shown that, in oxygen-free and iron rich conditions, RNAs would happily work with iron instead and that its presence could speed up their catalytic activity.

Now the group is back with a new paper showing that if you put a bunch of random RNAs into the same conditions, some of them can catalyze electron transfer reactions. By “random,” I mean RNAs that are currently used by cells to do completely unrelated things (specifically, ribosomal and transfer RNAs). The reactions they catalyze are very simple, but remember: these RNAs don’t normally function as a catalyst at all. It wouldn’t surprise me if, after a number of rounds of evolutionary selection, an iron-RNA combination could be found that catalyzes a reaction that’s a lot closer to modern metabolism.

All of which suggests that the basics of a metabolism could have gotten started without proteins around.

Proteins build membranes

Clearly, proteins showed up at some point. They certainly didn’t look much like the proteins we see today, which may have hundreds or thousands of amino acids linked together. In fact, they may not have looked much like proteins at all, if a paper from Jack Szostak’s group is any indication. Szostak’s found that just two amino acids linked together may have catalytic activity. Some of that activity can help them engage in competition over another key element of the first cells: membrane material.

The work starts with a two amino acid long chemical called a peptide. If that peptide happens to be serine linked to histidine (two amino acids in use by life today), it has an interesting chemical activity: very slowly and poorly, it links other amino acids together to form more peptides. This weak activity is especially true if the amino acids are phenylalanine and leucine, two water-hating chemicals. Once they’re linked, they will precipitate out of a water solution.

The authors added a fatty acid membrane, figuring that it would soak up the reaction product. That definitely worked, with the catalytic efficiency of serine-histidine going up as a result. But something else happened as well: membranes that incorporated the reaction product started growing. It turns out that its presence in the membrane made it an efficient scrounger of other membrane material. As they grew, these membranes extended as long filaments that would break up into smaller parts with a gentle agitation and then start growing all over again.

In fact, the authors could set up a bit of a Darwinian competition between membranes based on how much starting catalyst each had. All of which suggests that proteins might have found their way into the cell as very simple chemicals that, at least initially, weren’t in any way connected to genetic and biochemical functions performed by RNA. But any cell-like things that evolved an RNA that made short proteins could have a big advantage over its competition.

Read the entire article here.

Technica

Shakespearian Sonnets Now Available on DNA

Shakespeare meet thy DNA. The most famous literary figure in the English language had a recent rendezvous with that most famous and studied of molecules. Together chemists, cell biologists, geneticists and computer scientists are doing some amazing things — storing information using the base-pair sequences of amino-acids on the DNA molecule.

[div class=attrib]From ars technica:[end-div]

It’s easy to get excited about the idea of encoding information in single molecules, which seems to be the ultimate end of the miniaturization that has been driving the electronics industry. But it’s also easy to forget that we’ve been beaten there—by a few billion years. The chemical information present in biomolecules was critical to the origin of life and probably dates back to whatever interesting chemical reactions preceded it.

It’s only within the past few decades, however, that humans have learned to speak DNA. Even then, it took a while to develop the technology needed to synthesize and determine the sequence of large populations of molecules. But we’re there now, and people have started experimenting with putting binary data in biological form. Now, a new study has confirmed the flexibility of the approach by encoding everything from an MP3 to the decoding algorithm into fragments of DNA. The cost analysis done by the authors suggest that the technology may soon be suitable for decade-scale storage, provided current trends continue.

Trinary encoding

Computer data is in binary, while each location in a DNA molecule can hold any one of four bases (A, T, C, and G). Rather than using all that extra information capacity, however, the authors used it to avoid a technical problem. Stretches of a single type of base (say, TTTTT) are often not sequenced properly by current techniques—in fact, this was the biggest source of errors in the previous DNA data storage effort. So for this new encoding, they used one of the bases to break up long runs of any of the other three.

(To explain how this works practically, let’s say the A, T, and C encoded information, while G represents “more of the same.” If you had a run of four A’s, you could represent it as AAGA. But since the G doesn’t encode for anything in particular, TTGT can be used to represent four T’s. The only thing that matters is that there are no more than two identical bases in a row.)

That leaves three bases to encode information, so the authors converted their information into trinary. In all, they encoded a large number of works: all 154 Shakespeare sonnets, a PDF of a scientific paper, a photograph of the lab some of them work in, and an MP3 of part of Martin Luther King’s “I have a dream” speech. For good measure, they also threw in the algorithm they use for converting binary data into trinary.

Once in trinary, the results were encoded into the error-avoiding DNA code described above. The resulting sequence was then broken into chunks that were easy to synthesize. Each chunk came with parity information (for error correction), a short file ID, and some data that indicates the offset within the file (so, for example, that the sequence holds digits 500-600). To provide an added level of data security, 100-bases-long DNA inserts were staggered by 25 bases so that consecutive fragments had a 75-base overlap. Thus, many sections of the file were carried by four different DNA molecules.

And it all worked brilliantly—mostly. For most of the files, the authors’ sequencing and analysis protocol could reconstruct an error-free version of the file without any intervention. One, however, ended up with two 25-base-long gaps, presumably resulting from a particular sequence that is very difficult to synthesize. Based on parity and other data, they were able to reconstruct the contents of the gaps, but understanding why things went wrong in the first place would be critical to understanding how well suited this method is to long-term archiving of data.

[div class=attrib]Read the entire article following the jump.[end-div]

[div class=attrib]Image: Title page of Shakespeare’s Sonnets (1609). Courtesy of Wikipedia / Public Domain.[end-div]

BigBang

Evolution and Autocatalysis

A clever idea about the process of emergence from mathematicians at the University of Vermont has some evolutionary biologists thinking.

[div class=attrib]From MIT Review:[end-div]

One of the most puzzling questions about the origin of life is how the rich chemical landscape that makes life possible came into existence.

This landscape would have consisted among other things of amino acids, proteins and complex RNA molecules. What’s more, these molecules must have been part of a rich network of interrelated chemical reactions which generated them in a reliable way.

Clearly, all that must have happened before life itself emerged. But how?

One idea is that groups of molecules can form autocatalytic sets. These are self-sustaining chemical factories, in which the product of one reaction is the feedstock or catalyst for another. The result is a virtuous, self-contained cycle of chemical creation.

Today, Stuart Kauffman at the University of Vermont in Burlington and a couple of pals take a look at the broader mathematical properties of autocatalytic sets. In examining this bigger picture, they come to an astonishing conclusion that could have remarkable consequences for our understanding of complexity, evolution and the phenomenon of emergence.

They begin by deriving some general mathematical properties of autocatalytic sets, showing that such a set can be made up of many autocatalytic subsets of different types, some of which can overlap.

In other words, autocatalytic sets can have a rich complex structure of their own.

They go on to show how evolution can work on a single autocatalytic set, producing new subsets within it that are mutually dependent on each other.  This process sets up an environment in which newer subsets can evolve.

“In other words, self-sustaining, functionally closed structures can arise at a higher level (an autocatalytic set of autocatalytic sets), i.e., true emergence,” they say.

That’s an interesting view of emergence and certainly seems a sensible approach to the problem of the origin of life. It’s not hard to imagine groups of molecules operating together like this. And indeed, biochemists have recently discovered simple autocatalytic sets that behave in exactly this way.

But what makes the approach so powerful is that the mathematics does not depend on the nature of chemistry–it is substrate independent. So the building blocks in an autocatalytic set need not be molecules at all but any units that can manipulate other units in the required way.

These units can be complex entities in themselves. “Perhaps it is not too far-fetched to think, for example, of the collection of bacterial species in your gut (several hundreds of them) as one big autocatalytic set,” say Kauffman and co.

And they go even further. They point out that the economy is essentially the process of transforming raw materials into products such as hammers and spades that themselves facilitate further transformation of raw materials and so on. “Perhaps we can also view the economy as an (emergent) autocatalytic set, exhibiting some sort of functional closure,” they speculate.

[div class=attrib]Read the entire article after the jump.[end-div]