Posts about chemistry

How Lysozyme Protein in Our Tear-Drops Kill Bacteria

A disease-fighting protein in our teardrops has been tethered to a tiny transistor, enabling UC Irvine scientists to discover exactly how it destroys dangerous bacteria. The research could prove critical to long-term work aimed at diagnosing cancers and other illnesses in their very early stages.

Ever since Nobel laureate Alexander Fleming found that human tears contain antiseptic proteins called lysozymes about a century ago, scientists have tried to solve the mystery of how they could relentlessly wipe out far larger bacteria. It turns out that lysozymes have jaws that latch on and chomp through rows of cell walls like someone hungrily devouring an ear of corn.

“Those jaws chew apart the walls of the bacteria that are trying to get into your eyes and infect them,” said molecular biologist and chemistry professor Gregory Weiss, who co-led the project with associate professor of physics & astronomy Philip Collins.

The researchers decoded the protein’s behavior by building one of the world’s smallest transistors – 25 times smaller than similar circuitry in laptop computers or smartphones. Individual lysozymes were glued to the live wire, and their eating activities were monitored.

“Our circuits are molecule-sized microphones,” Collins said. “It’s just like a stethoscope listening to your heart, except we’re listening to a single molecule of protein.”

It took years for the UCI scientists to assemble the transistor and attach single-molecule teardrop proteins. The scientists hope the same novel technology can be used to detect cancerous molecules. It could take a decade to figure out but would be well worth it, said Weiss, who lost his father to lung cancer.

“If we can detect single molecules associated with cancer, then that means we’d be able to detect it very, very early,” Weiss said. “That would be very exciting, because we know that if we treat cancer early, it will be much more successful, patients will be cured much faster, and costs will be much less.”

The project was sponsored by the National Cancer Institute and the National Science Foundation. Co-authors of the Science paper are Yongki Choi, Issa Moody, Patrick Sims, Steven Hunt, Brad Corso and Israel Perez.

Related: full press releaseWhy ‘Licking Your Wounds’ WorksHow Bleach Kills BacteriaAlgorithmic Self-Assembly

Cooking with Chemistry: Hard Candy

The video by Richard Hartel, professor of food engineering at the University of Wisconsin-Madison, demonstrates how the molten liquid candy cools to form what from a technical standpoint actually is a glass. Unlike window glass made of silica, this tasty glass is made of sugar.

Viscosity describes a fluid’s internal resistance to flow and may be thought of as a measure of fluid friction. Water has very little viscosity (unless it is frozen). Thick honey has higher viscosity (especially if it is cooler – I keep my honey in the fridge and it does not flow very quickly).

As I have said before if I had understood the chemistry behind cooking as a kid I think I would have been much more interested in cooking.

Related: Understanding the Chemistry Behind CookingThe Man Who Unboiled an EggTracking the Ecosystem Within Us

Periodic Table for Kids

Poster of the periodic table with some illustrations and explanations for kids.

Check out this previous post with a New Visualization of the Periodic Table and see the link in the comment to another variation.

Related: Understanding the Chemistry Behind Cooking2009 Nobel Prize in Chemistry

2011 Nobel Prize in Chemistry

photo of Dan Shechtman

Dan Shechtman, Israel Institute of Technology, 2011 Nobel Laurette in Chemistry

The Royal Swedish Academy of Sciences has decided to award the Nobel Prize in Chemistry for 2011 to Dan Shechtman, Technion – Israel Institute of Technology, Haifa, Israel for the discovery of quasicrystals.

In quasicrystals, we find the fascinating mosaics reproduced at the level of atoms: regular patterns that never repeat themselves. However, the configuration found in quasicrystals was considered impossible, and Dan Shechtman had to fight a fierce battle against established science. The Nobel Prize in Chemistry 2011 has fundamentally altered how chemists conceive of solid matter.

On the morning of 8 April 1982, an image counter to the laws of nature appeared in Dan Shechtman’s electron microscope. In all solid matter, atoms were believed to be packed inside crystals in symmetrical patterns that were repeated periodically over and over again. For scientists, this repetition was required in order to obtain a crystal.

Shechtman’s image, however, showed that the atoms in his crystal were packed in a pattern that could not be repeated. Such a pattern was considered just as impossible as creating a football using only six-cornered polygons, when a sphere needs both five- and six-cornered polygons. His discovery was extremely controversial. In the course of defending his findings, he was asked to leave his research group. However, his battle eventually forced scientists to reconsider their conception of the very nature of matter.

Aperiodic mosaics, such as those found in the medieval Islamic mosaics of the Alhambra Palace in Spain and the Darb-i Imam Shrine in Iran, have helped scientists understand what quasicrystals look like at the atomic level. In those mosaics, as in quasicrystals, the patterns are regular – they follow mathematical rules – but they never repeat themselves.

When scientists describe Shechtman’s quasicrystals, they use a concept that comes from mathematics and art: the golden ratio. This number had already caught the interest of mathematicians in Ancient Greece, as it often appeared in geometry. In quasicrystals, for instance, the ratio of various distances between atoms is related to the golden mean.

Following Shechtman’s discovery, scientists have produced other kinds of quasicrystals in the lab and discovered naturally occurring quasicrystals in mineral samples from a Russian river. A Swedish company has also found quasicrystals in a certain form of steel, where the crystals reinforce the material like armor. Scientists are currently experimenting with using quasicrystals in different products such as frying pans and diesel engines.

Related: 2009 Nobel Prize in Chemistry: the Structure and Function of the RibosomeThe Nobel Prize in Chemistry 2008Nobel Prize in Chemistry (2006)

Read more on the science he has worked on. Our understanding of science is built on the discoveries of our predecessors and on the discoveries that counter what we thought we knew.
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New Analysis of Primordial Soup Experiment Half a Century Later

Open access paper: Primordial synthesis of amines and amino acids in a 1958 Miller H2S-rich spark discharge experiment

Archived samples from a previously unreported 1958 Stanley Miller electric discharge experiment containing hydrogen sulfide (H2S) were recently discovered and analyzed using high-performance liquid chromatography and time-of-flight mass spectrometry. We report here the detection and quantification of primary amine-containing compounds in the original sample residues, which were produced via spark discharge using a gaseous mixture of H2S, CH4, NH3, and CO2. A total of 23 amino acids and 4 amines, including 7 organosulfur compounds, were detected in these samples.

The major amino acids with chiral centers are racemic within the accuracy of the measurements, indicating that they are not contaminants introduced during sample storage. This experiment marks the first synthesis of sulfur amino acids from spark discharge experiments designed to imitate primordial environments. The relative yield of some amino acids, in particular the isomers of aminobutyric acid, are the highest ever found in a spark discharge experiment.

The simulated primordial conditions used by Miller may serve as a model for early volcanic plume chemistry and provide insight to the possible roles such plumes may have played in abiotic organic synthesis. Additionally, the overall abundances of the synthesized amino acids in the presence of H2S are very similar to the abundances found in some carbonaceous meteorites, suggesting that H2S may have played an important role in prebiotic reactions in early solar system environments.

Related: All present-day Life on Earth Has A Single AncestorLife Untouched by the SunAmazing Designs of LifeAlbert Einstein, Marylin Monroe Hybrid Image

Scientific Inquiry: Arsenic for Phosphorus in Bacteria Cells

As would be expected with significant new scientific claims, scientists are examining the evidence. On her blog, Rosie Redfield, who runs a microbiology research lab in the Life Sciences Centre at the University of British Columbia, disputes NASA’s recent claims. This is how science is suppose to work. Scientists provide evidence. Other scientists review the evidence, try to verify the claims with experiments of their own and the scientific inquiry process moves toward new knowledge.

Arsenic-associated bacteria (NASA’s claims)

NASA’s shameful analysis of the alleged bacteria in the Mars meteorite made me very suspicious of their microbiology, an attitude that’s only strengthened by my reading of this paper. Basically, it doesn’t present ANY convincing evidence that arsenic has been incorporated into DNA (or any other biological molecule).

The authors then grew some cells with radioactive arsenate (73-As) and no phosphate, washed and dissolved them, and used extraction with phenol and phenol:chloroform to separate the major macromolecules. The protein fraction at the interface between the organic and aqueous phases had about 10% of the arsenic label but, because the interface material is typically contaminated with liquid from the aqueous phase, this is not good evidence that the cells’ protein contained covalently-bound arsenate in place of phosphorus. About 75% of the arsenic label was in the ‘supernatant ‘fraction. The authors describe this fraction as DNA/RNA, but it also contains most of the small water-soluble molecules of the cell, so its high arsenic content is not evidence that the DNA and RNA contain arsenic in place of phosphorus. The authors use very indirect evidence to argue that the distribution of arsenic mirrors that expected for phosphate, but this argument depends on so many assumptions that it should be ignored.

I don’t know whether the authors are just bad scientists or whether they’re unscrupulously pushing NASA’s ‘There’s life in outer space!’ agenda. I hesitate to blame the reviewers, as their objections are likely to have been overruled by Science’s editors in their eagerness to score such a high-impact publication.

New claims have to provide strong evidence. time will tell if this discovery is actually a discovery. It will be amazing if it is, so I am pulling for it. But the story will need to have much more confirmation before we can be certain.

Arsenate-based DNA: a big idea with big holes

The study published in Science has a number of flaws. In particular, one subtle but critical piece of evidence has been overlooked, and it demonstrates that the DNA in question actually has a phosphate – not an arsenate -backbone.

Wolfe-Simon et al. used a technique called nanoSIMS to analyze elemental concentrations of the agarose gel at the location of the DNA band. They determined that the part of the gel containing DNA also contained both arsenic and phosphorus. But what did they really analyze?

The answer is that the nanoSIMS determined the concentration of arsenic in the gel – not specifically in the DNA.

Finally, there’s a simple experiment that could resolve this debate: analyze the nucleotides directly. Show a mass spectrum of DNA sequences demonstrating that nucleotides contain arsenate instead of phosphate. This is a very simple experiment, and would be quite convincing – but it has not been performed.

Related: It’s not an arsenic-based life formMono Lake bacteria build their DNA using arsenicClose Encounters of the Media Kind

Changing Life as We Know It

Update: Independent researchers find no evidence for arsenic life in Mono Lake

NASA has made a discovery that changes our understanding of the very makeup of life itself on earth. I think my favorite scientific discipline name is astrobiology. NASA pursues a great deal of this research not just out in space but also looking at earth based life. Their astrobiology research has changed the fundamental knowledge about what comprises all known life on Earth.

photo of Felisa Wolfe-Simon

Felisa Wolfe-Simon processing mud from Mono Lake to inoculate media to grow microbes on arsenic.

Carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur are the six basic building blocks of all known forms of life on Earth. Phosphorus is part of the chemical backbone of DNA and RNA, the structures that carry genetic instructions for life, and is considered an essential element for all living cells.

Phosphorus is a central component of the energy-carrying molecule in all cells (adenosine triphosphate) and also the phospholipids that form all cell membranes. Arsenic, which is chemically similar to phosphorus, is poisonous for most life on Earth. Arsenic disrupts metabolic pathways because chemically it behaves similarly to phosphate.

Researchers conducting tests in the harsh, but beautiful (see photo), environment of Mono Lake in California have discovered the first known microorganism on Earth able to thrive and reproduce using the toxic chemical arsenic. The microorganism substitutes arsenic for phosphorus in its cell components.

“The definition of life has just expanded,” said Ed Weiler, NASA’s associate administrator for the Science Mission Directorate. “As we pursue our efforts to seek signs of life in the solar system, we have to think more broadly, more diversely and consider life as we do not know it.” This finding of an alternative biochemistry makeup will alter biology textbooks and expand the scope of the search for life beyond Earth.

In science such huge breakthroughs are not just excepted without debate, however, which is wise.

Thriving on Arsenic:

In other words, every experiment Wolfe-Simon performed pointed to the same conclusion: GFAJ-1 can substitute arsenic for phosphorus in its DNA. “I really have no idea what another explanation would be,” Wolfe-Simon says.

But Steven Benner, a distinguished fellow at the Foundation for Applied Molecular Evolution in Gainesville, FL, remains skeptical. If you “replace all the phosphates by arsenates,” in the backbone of DNA, he says, “every bond in that chain is going to hydrolyze [react with water and fall apart] with a half-life on the order of minutes, say 10 minutes.” So “if there is an arsenate equivalent of DNA in that bug, it has to be seriously stabilized” by some as-yet-unknown mechanism.

It is sure a great story if it is true though. Other scientists will examine more data and confirm or disprove the claims.

“We know that some microbes can breathe arsenic, but what we’ve found is a microbe doing something new — building parts of itself out of arsenic,” said Felisa Wolfe-Simon, a NASA Astrobiology Research Fellow in residence at the U.S. Geological Survey in Menlo Park, Calif., and the research team’s lead scientist. “If something here on Earth can do something so unexpected, what else can life do that we haven’t seen yet?”
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Understanding the Chemistry Behind Cooking

Video either broken by bigthink or their system is extremely poor causing minutes of failure to load 🙁 Removed.

The science behind cooking is very interesting. I would have been more interested in cooking if I was exposed to more of this early on in my life.

Related: The Man Who Unboiled an EggDon’t Eat What Doesn’t RotRethinking the Food Production SystemThe Calorie DelusionTracking the Ecosystem Within Us

Ants, Ants, Ants

Ants really are amazing. The internet makes it easy to learn about these creatures. My Dad found them fascinating and I picked up that view. I had a flying one, flying around my house yesterday.

“Ants: The Invisible Majority” including Dr. Brian Fisher, chairman of the Department of Entomology at the Cal Academy of Sciences looking for ants in San Francisco. He created AntWeb, an online resource. The video discusses the Argentine Ant super colonies.

Related: Ants Counting Their StepsE.O. Wilson: Lord of the AntsSymbiotic relationship between ants and bacteria

Briggs-Rauscher Oscillating Reaction

video showing the Briggs-Rauscher Oscillating Reaction. From Wikipedia:

The first known homogeneous oscillating chemical reaction, reported by W. C. Bray in 1921, was between hydrogen peroxide (H2O2) and iodate (IO3−) in acidic solution. Due to experimental difficulty, it attracted little attention and was unsuitable as a demonstration. In 1958 B. P. Belousov in the Soviet Union discovered the Belousov–Zhabotinsky reaction (BZ reaction), is suitable as a demonstration, but it too met with skepticism (largely because such oscillatory behavior was unheard of up to that time) until A. M. Zhabotinsky, also in the USSR, learned of it and in 1964 published his research. In May of 1972 a pair of articles in the Journal of Chemical Education brought it to the attention of two science instructors at Galileo High School in San Francisco. They discovered the Briggs–Rauscher oscillating reaction by replacing bromate (BrO3−) in the BZ reaction by iodate and adding hydrogen peroxide. They produced the striking visual demonstration by adding starch indicator.

The detailed mechanism of this reaction is quite complex. Nevertheless, a good general explanation can be given.
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Zubbles – Get Your Colored Bubbles

photo of blue bubblephoto of blue colored bubble.

I first posted on this in 2005: Colored Bubbles. Now you can order your own via Zubbles. Colored Bubbles Have Landed (and Popped and Vanished)

Having solved the colored bubble dilemma, we spent most of 2006 trying to refine our dyes and the manufacturing process. We had invented several completely new dyes and a few derivatives of existing dyes. But the manufacturing process was long, tedious and expensive. It took three days just to make a few grams of each dye. It quickly became apparent that we needed to radically streamline the production process in order to have a viable product.

The complexities of the chemistry resembled a pharmaceutical more than a toy. So I enlisted the help of Gary Willingham, and the Belgium development team, at Fisher Scientific. Fisher is a pharmaceutical chemical manufacturer with the equipment and expertise needed to manufacture tons of our dyes.

Due to the complexities of the chemistry, Jamm decided to stay close to the production process and manufacture Zubbles in the US. The first bottles rolled off the line this week. Jamm presented me with the very first case of Zubbles. And it was a very strange feeling to finally hold the product in my hand—15 years after I mixed my first batch of dishwashing detergent and food coloring.

Being an entrepreneur is a challenge any time. When your product requires complex science and engineering that adds additional challenges. It is great to see this product is now available.

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