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Breaking Down Sugars

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Today is Valentine’s Day, which means you might have just spent the morning rushing around for last minute treats to gift to your loved one. But not all sweet treats are made alike. What is the difference between sugar, artificial sweeteners, and that old American favorite, high fructose corn syrup? And what happens when we try to digest them?

Chemically, sugars are a type of carbohydrate, a compound made from chains of carbon, oxygen, and hydrogens. Carbohydrates are also sometimes called saccharides, and they serve a range of functions in the body, including storing energy. They are classified by how long their chains are. Monosaccharides, also known as simple sugars, are a single unit of a chain. These monosaccharides are chained together to form other, more complex sugars. For example, refined or table sugar is made from sucrose, a disaccharide comprised of fructose and glucose, both monosaccharides. Sucrose can be refined from cane plants or from sugar beet and is a source of pure carbohydrates. There are also oligosaccharides and polysaccharides, which are made of even longer chains of simple sugars. When the more complex sugars are broken down in the body, they are broken down into their constituent monosaccharides, or for the longer and more complex carbohydrates, even disaccharides or oligosaccharides (3-10 units).

Types of Sugars
Source: PubMed Health, PubMed, and Tymoczko, John L., Lubert Stryer, and Gregory J. Gatto, Jr. “Glycolysis and Glucogenesis.” Biochemistry. By Jeremy M. Berg. 7th ed. Houndsmills, England: W. H. Freeman, 2012. 469-507. Print.

Sucrose is a sweetener found in nature, but we can also manufacture other saccharide-based sweeteners. An example of this is high fructose corn syrup. It was developed because syrups are easier to handle than powders on a large scale, because they pour out better and are more containable. High fructose corn syrup is made from corn starch. Enzymes break down starch into fructose and oligosaccharides. Another enzyme, glucosidase is added to convert everything to glucose. Glucose and fructose have the same chemical formula—they have the same number of carbons, hydrogens, and oxygens but they are arranged differently. Glucose can be converted to fructose, and is even done so in the body. High fructose corn syrup, then, is a mixture of water, glucose, and fructose made from glucose.

Perhaps the most [in]famous of artificial sweeteners is aspartame, which can be found in Diet Coke.

There are also artificial sweeteners, food additives designed to add sweetness without the additional Calories. Perhaps the most [in]famous of artificial sweeteners is aspartame, which can be found in Diet Coke and commercially as NutraSweet. Aspartame is a methyl ester of a dipeptide, which means it is made of two amino acids with an additional group stuck on the end. The structure of aspartame is very different from sugar, especially metabolically since it is made of protein subunits.

Aspartame is broken down very quickly in the body into aspartic acid, phenylalanine, and methanol. The former two are essential amino acids, and the methanol is eventually converted into formic acid, which passes through the body. All three could be toxic in large quantities, but numerous studies suggest that aspartame is safe for human health. However, because it’s broken down so quickly and contains none of those high energy carbs, aspartame and other artificial sweeteners satisfy a sweet tooth without any Caloric benefit (depending on your point of view).

Sugar in the Body Valentines Day by The Stem Chicks
Source: Tymoczko, John L., Lubert Stryer, and Gregory J. Gatto, Jr. “Glycolysis and Glucogenesis.” Biochemistry. By Jeremy M. Berg. 7th ed. Houndsmills, England: W. H. Freeman, 2012. 469-507. Print.

So, what happens when we eat something with real sugar, ie saccharides, in it? Let’s take a Sweetheart, made from sugar, corn syrup, gelatin, gums, coloring and flavoring. For some sugars, digestion starts in the mouth. Amalyses  in the saliva break down complex starches into disaccharides, which are then eventually cleaved into glucose. The corn syrup might have some residual starch, so some will be broken down here. The sugars will continue their way down the digestive track to the small intestine, where they encounter the enzyme sucrase. Sucrase breaks the sucrose into fructose and glucose. At this point the two diverge. Fructose must pass through the liver, where it’s converted into a variety of products, including glucose and lactate. Eating sugar causes a temporary spike in blood glucose or blood sugar levels, which is used by cells as an energy source. Glucose is converted into usable energy, or metabolized, through a series of complicated mechanisms called glycolysis and the Krebs cycle. You can read more here. The gist is, the glucose is oxidized and after a series of reactions makes CO2, water, nitrogen compounds and Gibbs free energy which can be used by the cells to function.

The different sugars we eat affect our body differently. High fructose corn syrup, which has a high amount of free fructose, puts a higher demand on the liver than normal sugar. Aspartame passes through the body with little metabolism at all. So today, when you give chocolate or candies to your loved one, tell them about the metabolism of sugars—I’m sure they’ll appreciate you for it 🙂

The STEM Chicksmas Day 12: The Structure of Ribosomes

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For the 12 Days of “The STEM Chicksmas” we’re highlighting 12 scientists who have contributed something innovative and exciting to their field. It is the season of giving, and these brilliant minds have given incredible gifts to the scientific community! This year we’re looking at 12 Nobel Prize winners from the past 15 years in the fields of Physics, Chemistry, and Physiology or Medicine.

Day Twelve: The 2009 Nobel Prize in Chemistry.

The STEM Chicksmas Nobel Prize 2009 Chemistry
Source: Nobel Prize Summary and Nobel Prize Popular Information

Form follows function—or maybe it’s the other way around.  Either way, one of the biggest keys to truly understanding the function of a molecule lies in understanding the atoms that make it up. For this reason, it has been a subject of great interest to find the underlying chemistry of various biological structures, like proteins. One way of doing this is by x-ray crystallography, a technique that uses the diffraction of x-rays to make a picture of the location of all the atoms in a structure. The problem, of course, lies in the size of biological structures. Unlike small molecules, which might contain only a few atoms (water has 3, for example), biological structures contain thousands. Mapping every single one of these atoms is no easy feat—yet the winners of the 2009 Nobel Prize in Chemistry, Venkataraman Ramakrishnan, Thomas A. Steitz, and Ada Yonath manage to succeed in mapping the structure of the ribosome.

Ribosomes are important in the process of encrypting new proteins with genetic information. The attach nucleic acids in the order specified by messenger RNA (to read more about the role of mRNA check out our post here). The ribosome binds to the mRNA, which carries a genetic template, and amino acids are carried to the ribosome by another type of RNA, transfer RNA. The ribosome then links together the amino acids to make a protein! It is an extremely complicated structure with two subunits: in humans the small subunit is made of one RNA molecule and 32 proteins, and the large subunit is made of 3 RNA molecules and 46 proteins. This adds up to hundreds of thousands of atoms….but in the 1970s Yonath decided to map them using x-ray crystallography.

X-ray crystallography is a method to determine the structure of a crystal (read more on our post about quasicrystals here). However, to do x-ray crystallography, the structure has to be crystalline…but most biological structures are aqueous and do not easily crystallize and often fall apart in non in vivo conditions. This was the first of the many problems  biochemists faced. It took Yonath 20 years to make a crystal that was of good enough quality to make a clean diffraction pattern.

There arose a new problem: x-ray crystallography yields a diffraction pattern, which is a pattern of dots that yield information about the placement of the atoms. However, to correctly interpret these dots, their “phase angle” had to be determined. Because ribosomes were too large for the normal trick of determining phase angles to be utilized (attaching heavy atoms to the composite atoms), a new method had to be devised. In came Steitz, who used electron microscopy to find the orientation of the ribosomes in the crystals. This helped solve the phase angle problem. With Steitz’s help and Yonath’s years of hard work, the three scientists published good crystal structures of the ribosome within a few months of each other in the year 2000.

These structures were crucial for fully understanding the function of the ribosome.  Ramakrishnan discovered nucleotides on the small subunit that measure the distance between structures on the mRNA and the transfer RNA, which helps prevents errors in transferring information. Steitz helped pinpoint atoms that are important in the ribosome’s chemical reactions and in explaining how those reactions occur. These three scientists’ years of hard work explained the structure of the ribosome, and they also contributed to our ability to find the structure for biological molecules. The strides they’ve made, in both form and function, have truly been a gift to our scientific knowledge.

To learn more, check out the Nobel Prize website or the award winning work here (Ramakrishnan), here (Yonath), or here (Steitz)

The STEM Chicksmas Day Eleven: Telomerase

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For the 12 Days of “The STEM Chicksmas” we’re highlighting 12 scientists who have contributed something innovative and exciting to their field. It is the season of giving, and these brilliant minds have given incredible gifts to the scientific community! This year we’re looking at 12 Nobel Prize winners from the past 15 years in the fields of Physics, Chemistry, and Physiology or Medicine.

Day Eleven: The 2009 Nobel Prize in Physiology or Medicine.

The STEM Chicksmas Nobel Prize 2009 Medicine or Physiology
Source: Nobel Prize Summary and Nobel Prize Popular Information

In cell mitosis, the process by which a cell divides, the parent cell yields two genetically identical daughter cells, meaning they have identical DNA. But how? Why aren’t the chromosomes, which are packaged up DNA strands, degraded and shortened? It turns out that they are—but not quite in the way we would expect. The discovery of the roles of telomeres and telomerase by Elizabeth H. Blackburn, Carol W. Greider, and Jack W. Szostak won the 2009 Nobel Prize in Medicine.

The problem with chromosomes shortening comes down to the way DNA is copied. During mitosis, the double-stranded DNA is separated into a leading strand and a lagging strand. The leading strand is copied (for simplicity, we say “copied,” but the process actually copies the complement, more accurately termed replication) all at once, whereas the lagging strand has to be copied in short segments by an enzyme called DNA polymerase. However, the polymerase cannot just start copying the DNA. Instead, it needs a single-stranded primer made out of RNA to bind to the lagging template DNA. The polymerase can then copy the fragments, and the gaps in between the fragments are later filled in when the RNA primer is removed. However, the gap caused by the RNA primer at the end of the strand cannot be filled in, meaning that there is always a gap at the end of the copied chromosome. Despite this gap our DNA seems to be being copied correctly.

In the early 1900s cell biologists hypothesized that telomeres might play a protective role, because they observed that they prevented chromosomes from bonding together. Telomeres are the bits at the end of the chromosome, and in the 1970s Blackburn discovered that they contain a genetic sequence that repeats over and over again, 20-70 times, differing between chromosomes. Why were they different lengths?

More confusion arose when Blackburn and Szostak were working on yeast cells, trying to see what happened with these telomeres. They found that when DNA was replicated, it was not only truncated but could also grow longer. This was a confusing conclusion, because it went against the way DNA replication was understood at that time. Furthermore, the part that was added onto the sequence didn’t seem to come from a replication of original template DNA, but rather from an extension of the parent strand. A breakthrough came when Blackburn’s graduate student, Greider, designed a clever experiment. She made an extract of a certain type of cell, Tetrahymena, and mixed it with radioactively tagged nucleotides (building blocks of DNA) and artificial telomere DNA. The radioactively tagged nucleotides ended up being assembled in the same sequenceas those naturally occurring in Tetrahymenda. This led to the discovery of the enzyme telomerase. Telomerase adds telomeres onto the end of chromosomal strands based on its biological own sequence. This is why telomerase in the cell extract added the same telomeric sequence characteristic of Tetrahymenda to the ends of the artificial telomeres, using the radioactively tagged nucleotides. This prevents the problem of the gap that occurs when replicating DNA by lengthening the chromosome before replication!

The discovery of telomerase has given a lot of insight into how DNA replicates. Since then, researchers have found that cells in older organisms have chromosomes with truncated telomeres. It is possible that the telomere length and aging are related. Furthermore, because telomerase allows multiple divisions of a cell, high telomerase activity can allow unlimited division, leading to cancer. This would have never been recognized without the discovery of telomerase. We can now better investigate the cause of diseases, especially congenital diseases, expanding our knowledge and possibly leading to a cure.

To read more, check out the Nobel Prize website or the award winning work here.

The STEM Chicksmas Day Ten: Graphene

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For the 12 Days of “The STEM Chicksmas” we’re highlighting 12 scientists who have contributed something innovative and exciting to their field. It is the season of giving, and these brilliant minds have given incredible gifts to the scientific community! This year we’re looking at 12 Nobel Prize winners from the past 15 years in the fields of Physics, Chemistry, and Physiology or Medicine.

Day Ten: The 2010 Nobel Prize in Physics.

Source: Nobel Prize Summary, Nobel Prize Speed Read, and Nobel Prize Popular Information

What if you could win a Nobel Prize with a pencil and some tape? The winners of the 2010 Nobel Prize Andre Geim and Konstantin Novoselov did just that. They isolated and characterized a structure called graphene from graphite, the stuff pencils are made from, discovering a new class of stable “two dimensional” materials.

Graphite is a layered material, unlike other crystal lattices which are made of unit cells that extend in three dimensions. Each layer of graphite is made up of carbons arranged in repeating hexagons, like a honeycomb. The layers are held together by van der Waals forces, which are relatively weak interatomic interactions. Scientists have been trying for decades to isolate a single layer of graphite, called graphene, without success. Geim and Novoselov succeeded through a simple method called “exfoliation.” You lay a piece of scotch tape down on a piece of graphite. You then stick and unstick the scotch tape with a second piece of scotch tape over and over, each time yielding fewer layers of carbon, until you have a single layer. The mechanical strength of sticking and unsticking the tape is enough to overcome the van der Waals interactions without disrupting the stronger covalent bonds within the layer. This layer is “two dimensional”—it has macroscopic width and length, but it is only one atom thick. Consequently, its properties only extend in two dimensions, making it for all intents and purposes two dimensional.

Geim and Novoselov’s method was also remarkable because of the surface area it was able to produce. They were able to produce reliably large areas of intact graphene with few or no defects. Because of this feat, they were able to characterize their material and perform various tests on it. They discovered that graphene is conductive (read more about conductivity in our post on conductive polymers). Graphene is also very mechanically strong. A common example people use is that a single sheet of graphene is strong enough to hold up a cat! At least, according to calculations, because we’ve never produced a sheet large enough to try. It is very flexible, partially because the intralayer bonding is so strong. Graphene is also almost transparent.

Graphene’s unique properties make it the source of a lot of research into future applications. One example is organic solar cells. Graphene is basically transparent, so it could be coated onto more conventional solar panels without preventing light from going through, and contribute its conductive properties to enhances the solar cell’s energy conversion efficiency. Another potential application is in electronics—we could use graphene to make flexible conductors. The future of graphene is very exciting and a common subject of research in materials and condensed matter physics. However, because it is currently impossible to produce industrial sized layers of graphene (the “large” layers mentioned earlier are a few microns wide), many of these applications remain theoretical. The discovery of graphene also showed that it is possible to make stable two dimensional materials, which was previously thought of as impossible. Two dimensional materials is a rising field that many scientists are studying intently (including this author’s former research group!).

The discovery of graphene has opened up exciting new research and pioneered new paths. However, best of all, it shows that science doesn’t always need fancy and expensive equipment—sometimes all you need is some household objects and ingenuity.

Read more at the Nobel Prize website or read the award winning work here.

The STEM Chicksmas Day 9: Conductive Polymers

The Stem Chicksmas Chemistry 2000
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For the 12 Days of “The STEM Chicksmas” we’re highlighting 12 scientists who have contributed something innovative and exciting to their field. It is the season of giving, and these brilliant minds have given incredible gifts to the scientific community! This year we’re looking at 12 Nobel Prize winners from the past 15 years in the fields of Physics, Chemistry, and Physiology or Medicine.

Day Nine: The 2000 Nobel Prize in Chemistry.

The STEM Chicksmas Nobel Prize 2000 Chemistry
Source: Nobel Prize Summary and Nobel Prize Popular Information

When we think of plastics, we generally think of them as insulators, materials that inhibit the flow of electrical current. A common application of this insulating ability is the plastic that coats wires to protect us from receiving a shock if we touch them. However, what if plastics could conduct electrical charge the way metals can? It turns out that certain plastics can conduct—but only if you make them correctly. This discovery by Alan J. Heeger, Alan G. MacDiarmid and Hideki Shirakawa earned the Nobel Prize in Chemistry in year 2000.

The conducting ability of a material is determined by its electronic structure. The energy of electrons is quantized, which means electrons can only be at certain energy levels. However, this also means that electrons cannot exist within a certain energy range. This forbidden energy range is called the band gap, and in solid materials it is the gap between the conduction and the valence band. The valence band is the band where electrons exist in a non-excited material. If a voltage is applied to the material and the band gap is small enough, electrons can jump to the conduction band. However, this is only possible if the valence band is not fully occupied. This movement of electrons is an electrical current! Using band gaps we can define three types of materials: conductors (no band gap, like metals), semi-conductors (a small band gap), and insulators (a very large band gap). In general, the longer a material is, the smaller the band gap gets. This is relevant when talking about plastics, because chain length is a very important factor.

When we talk about plastics we’re actually talking about polymers, very large molecules made up of a chain of repeating units. In organic polymers, this is a carbon chain. The unit can include double bonds, atoms such as oxygen or chloride, or functional groups like alcohols. The groups that are on the carbon chain determine its properties. The type of polymer the Nobel Prize winners looked at were organic polymers with alternating double bonds, specifically polyacetylene. They found that when they “doped” these polymers, they became conductive. When you dope a substance, you introduce a hole (“p-doping) or an electron (“n-doping”) into the chain via a chemical reaction, either reduction or oxidation. This is important because generally, carbon chains have fully occupied valence bands. If you p-dope it, you turn one of the double-bonds into a single electron. Since an electron is missing, it appears that you have a positive charge which we call the hole. The single electron and hole can move along the chain fairly easily. If you n-dope it, a more complicated mechanism causes the transport of charges across the molecule.

By discovering conductive plastics, Shirakawa et al revolutionized the future of electronics. Plastics are cheap and easy to produce, and making them conductive also is a fairly simple chemical reaction. They can potentially be used in organic solar cells and biosensors. It is difficult to scale up their processing to industrial scales, but if this can be achieved conductive polymers could be the future of our devices.

To read more, check out the Nobel Prize website here.

The STEM Chicksmas Day Eight: Cell Signaling

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For the 12 Days of “The STEM Chicksmas” we’re highlighting 12 scientists who have contributed something innovative and exciting to their field. It is the season of giving, and these brilliant minds have given incredible gifts to the scientific community! This year we’re looking at 12 Nobel Prize winners from the past 15 years in the fields of Physics, Chemistry, and Physiology or Medicine.

Day Eight: The 2000 Nobel Prize in Medicine or Physiology.

The STEM Chicksmas Nobel Prize 2000 Medicine or Physiology
Source: Nobel Prize Summary and Nobel Prize Speed Read

The 2000 Nobel Laureates in Medicine Arvid Carlsson, Paul Greengard, and Eric Kandel all made significant discoveries concerning signal transductions in the nervous system. “Signal transduction” is the process by which a stimulus outside the cell triggers a biochemical response inside the cell. The signaling molecule activates a receptor located on the cell. When this happens in the nervous system, for example in the brain, this process is referred to as synaptic- or neurotransmission. The cells in the nervous system, called neurons, oftentimes do not come into physical contact with each other. Instead they transmit information over a small gap, called the synapse, either chemically or  electrically. Chemical transmission is most prevalent in our bodies. One neuron will release neurotransmitters, which are chemical messengers that then bind to a receptor in the second neuron, activating it and eliciting a response. In the nervous system, these responses range from being able to move to being able to think to regulating all of your bodily responses. Understanding signal transduction in the nervous system and better understanding the nervous system in general brings us one step closer to being able to develop better medicine and therapeutic treatments.

Carlsson’s discovery had to do with dopamine’s important role in the brain. Many researchers previously thought that dopamine was a precursor to another type of neurotransmitter, noradrenaline (also known as norepinephrine), rather than being a neurotransmitter itself. However, Carlsson developed a selective test to locate dopamine, and he discovered that dopamine is actually localized in places where noradrenaline is not. To test what dopamine’s role might be, he injected animals with a cocktail of chemicals that froze neurotransmitter activity and consequently their physical movement. When injected with L-dopa, a chemical that converts to dopamine in the body, their movement miraculously returned! Carlsson’s discovery that dopamine plays a role in regulating motor skills is especially important because it led to a greater understanding of Parkinson’s disease, specifically Parkinson’s patients have a shortage of dopamine in a specific area of their brain. To this day, L-dopa is used as a treatment for Parkinson’s to regulate patients’ motor skills. Carlsson’s discovery was also vital for understanding and developing antipsychotics and antidepressives.

Greengard built off of Carlsson’s work. He investigated the mechanism by which neurotransmitters actually work—that is, what happens on the chemical level. He discovered that neurotransmitters like dopamine and serotonin work via slow synaptic transmission, where the change in the neuron may last anywhere from a few seconds to a few hours. This is important for mood, for example, whereas fast synaptic transmission regulates things like speech and actions. He found that this slow synaptic transmission is a mechanism that begins a chemical chain reaction. For instance, dopamine binds with a target receptor on a neuron, which causes the release of a second messenger molecule, which switches on a host of proteins quickly in a cascade reaction through a process called phosphorylation. In phosphorylation, a phosphate group (a group with phosphorous and oxygen) binds to a protein in such a way that it changes its function. One function it changes is the excitability of certain neurons. Excitability refers to the electrical impulse necessary to transfer information synaptically. When the excitability is changed, the neuron transfers information differently. This is important because it led to better understanding of how certain drugs work.

Kandel was interested in memory. He took an animal with a fairly simple nervous system, the sea slug, and applied to the nerve cells. He found that applying certain stimuli increased the protective reflex of the sea slug. Weak stimuli affected short term memory by changing the nerve channels locally. Essentially, phosphorylation and changes in the ion channels of the first cell caused it to release more neurotransmitter into the synaptic space. Therefore, as neurotransmitter levels were increased, the stimulus was increased. Stronger stimuli, on the other hand, changed the production of certain proteins in the synapse. This increased the size of the synapse (the gap between two neurons), which led to an increased synaptic function over the long term—i.e. long term memory! Kandel’s discovery led to an important insight into human memory: it is based in the synapses. We don’t yet understand memory, but Kandel has pointed us in the right direction.

Through the work of these three researchers, medicine has been improved, our understanding of how drugs work and thus our development of new drugs has increased, and we have been set on the path towards understanding complex memory in humans.

To read more, check out the Nobel Prize website or the winning work here (Carlsson), here (Greengard), or here (Kandel).

 

The STEM Chicksmas Day Seven: Neutrino Oscillations

The Stem Chicksmas Physics 2015
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For the 12 Days of “The STEM Chicksmas” we’re highlighting 12 scientists who have contributed something innovative and exciting to their field. It is the season of giving, and these brilliant minds have given incredible gifts to the scientific community! This year we’re looking at 12 Nobel Prize winners from the past 15 years in the fields of Physics, Chemistry, and Physiology or Medicine.

Day Seven: The 2015 Nobel Prize in Physics.

The STEM Chicksmas Nobel Prize 2015 Physics
Source: Nobel Prize Summary, Nobel Prize Popular Information, and Invisibles of European ITN

What’s your favorite flavor of neutrino? Neutrinos belong to a category of fundamental particles called leptons. (To read more about particles and their role in the Standard Model of physics, check out our post on the Higgs Boson.)  There are three types, or in physicist parlance “flavors” of leptons, the electron, muon, and tau particles. These flavors can be found in both neutral and charged particles—the charged particles are simply named after the flavor (e.g. electron) and the neutral particles are neutrinos (e.g. electron neutrinos).

Leptons only interact with three of the four fundamental forces: the weak force, gravity, and the electromagnetic force. Neutrinos, being neutral, do not interact with the electromagnetic force. Furthermore, the weak force is, as the name implies, weak and a short-range interaction, and gravity has a very weak effect at the subatomic level. Neutrinos thus pass through matter as if it weren’t there. Detecting them, even now, is not an easy task. So when scientists in the 60s noticed that they only detected one third of the total number of neutrinos they expected to come from the sun, they figured that there was a problem with their model or their detection techniques. However, this one third remained consistent. No research group could account for the missing two thirds empirically.

Two sources of neutrinos are solar fusion and cosmic radiation. Muon neutrinos, for example, come from cosmic radiation, whereas solar fusion only produces electron neutrinos. Some physicists speculated that neutrinos traveling from the sun “changed flavor” on their way to Earth, which is why we could not detect them. (The detection methods were usually specific to electron neutrinos.) However, this would only be possible if the neutrinos had mass, and according to the Standard Model they were massless.

Why? Something important to keep in mind is that in quantum physics, particles are also waves—this is called wave-particle duality. Light is the best known example—it is simultaneously a wave and a photon. Waves are also capable of interfering with each other. When two wavelengths travel at different frequencies, they go out of phase with each other. When waves are out of phase, the amplitudes and shape of the superimposed wave is like an average of the composite waves. This is relevant for neutrinos because neutrinos also oscillate. Because the three flavors of neutrons have slightly different masses, they also move through space at different rates and frequencies. The case for neutrinos is more complicated, because both mass and flavor (specifically the interaction with their charged counterpoints) affect their quantum mechanical properties. The result is, however, that as neutrinos move through space, they oscillate and change flavor. If you look at our graphic, you see that the peaks of the different neutrino flavors shift in relation to each other as they move across the x-axis. This happens only if neutrinos have mass.

2015 Nobel Laureates in Physics Takaaki Kajita and Arthur B. McDonald were able to prove that neutrinos have mass.  Kajita and McDonald worked at two different detectors. At the Super-Kamiokande, neutrinos passed through a tank of very pure water that was deep within the ground. When muon and electron neutrinos passed through the water, they would sometimes collide with an atom nucleus or an electron in the water. When they did this, they would make charged particles (muons and electrons). The charged particles would move faster than the speed of light in water (75% of the speed of light in vacuum), and generate a blue light called the Cherenkov light. This light could be measured by detectors in the tank and the neutrino source determined. One curious aspect was that there were way more muon-neutrinos coming from the atmosphere straight above the detector than from those that traveled through the earth, ie those that traveled a further distance. This was explained at the Sudbury National Observatory. They ran a similar experiment on electron neutrinos from solar radiation, and using heavy water (water with deuterium instead of hydrogen), they detected the full number of neutrinos suggested by the Standard Model in all three flavors, not just electron-neutrinos.

The discovery at the Super-Kamiokande suggested that the distance traveled was related to the flavor of neutrino expressed. This makes sense when considering the probability of neutrinos’ waves going out of phase. The discovery at the Sudbury National Observatory accounted for the infamous missing two thirds of neutrinos. The fact that neutrinos have mass is important because it violates certain ideas set forth by the Standard Model, such as lepton conservation. Furthermore, it is important because we still don’t fully understand the role neutrinos play in the universe. There are billions and billions of neutrinos, and we don’t really know what they do. Some theorize that neutrinos play a role with hot dark matter. However, discovering neutrinos have mass is one step forward towards fully understanding particles and the universe.

Read more at the Nobel Prize website or check out the award winning work here (Kajita) or here (McDonald).

The STEM Chicksmas Day Six: The God Particle

The Stem Chicksmas Physics 2013
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For the 12 Days of “The STEM Chicksmas” we’re highlighting 12 scientists who have contributed something innovative and exciting to their field. It is the season of giving, and these brilliant minds have given incredible gifts to the scientific community! This year we’re looking at 12 Nobel Prize winners from the past 15 years in the fields of Physics, Chemistry, and Physiology or Medicine.

Day Six: The 2013 Nobel Prize in Physics.

The STEM Chicksmas Nobel Prize 2013 Physics
Source: Nobel Prize Summary and Nobel Prize Popular Information

Have you ever thought about where mass comes from? The answer isn’t as obvious as it first seems. A theory called the Standard Model says the universe is made of 17 elementary particles called quarks, leptons, and bosons; and four fundamental forces called the gravitational, weak, electromagnetic, and strong forces. Electrons and neutrinos, for example, are both types of leptons and the protons and neutrons that make up atoms are themselves made from quarks and get their mass from quarks’ binding energy. A force is defined by an exchange of a type of boson called gauge bosons. For example, light is the exchange of photons, which are the bosons associated with the electromagnetic force. However, a problem with the Standard Model physicists struggled to explain is that none of these gauge bosons should have mass, but of the four gauge bosons, only photons are massless. So, where did their mass come from?

In 1964, the 2013 Nobel Laureates in Physics Peter Higgs and François Englert proposed the idea of a field that interacts with the bosons to give them mass. As the bosons move through this field, called the Higgs Field, they interact with it. The more strongly they interact with it, the more potential energy the field transfers to them. Because energy and mass are related, the more energy the particles get, the more mass they have. If the particle does not interact with the field, they are massless, like the photon. Here’s one way to picture this. Imagine a room full of scientists throwing a party. A grad student walks in, and no one pays her any attention because she’s just a grad student. Now imagine Einstein walks into the room. Everyone immediately mobs him and tries to engage him in conversation. Like a photon, the grad student passed through the room unnoticed, whereas Einstein, like the other gauge bosons, gained the “mass” of a bunch of physicists. This is one way of imagining the coupling of particles and the Higgs field.

However, proving the existence of the Higgs Field was not an easy task. To do so, physicists concentrated their efforts on finding a particle called the Higgs Boson. The Higgs Boson is a quantum excitation of the Higgs Field. If the Higgs Boson exists, the Higgs Field must exist as well. Much like how if we see a light it must come from a light source, if we see a Higgs Boson it must come from the Higgs Field. The Standard Model also predicts that the Higgs Boson should have certain properties, such as a mass of 125-127 Gev/c2, zero spin, and positive parity (which means that if you flip the orientation of space like in a mirror, the Higgs boson still acts the same). This is easier said than done. The Higgs Boson is now often referred to as the “God particle,” which appears to be named so because the Higgs Field gives mass to other particles. However, this name is actually an abbreviation—originally it was referred to as the goddamn particle, because it was so goddamn hard to find.

Experiments done at the Large Hadron Collider (LHC) near Geneva strongly suggested the existence of the Higgs field. The LHC is a particle collider, which means it operates by smashing high energy beams of protons together at very high velocities. Lower energy particle accelerators are used to make certain radioactive isotopes. However, the scientists working at the LHC had bigger fish to fry—they were looking for the Higgs Boson. A high energy particle collider is needed to find the Higgs boson since E=mc^2 means that the energy of the proton beams determines the mass of the particles it can create. The Higgs boson was predicted to have a relatively high mass so only the LHC had enough energy to produce it. In 2012, LHC scientists successfully discovered a particle that agreed with the Standard Model predictions– they discovered the Higgs Boson!

Discovery of the Higgs Boson is so exciting because it confirms a lot of fundamental questions about the universe. It validates the Standard Model and explains how certain particles get their mass. It also poses a lot of mathematical questions about symmetry. Scientists believe that the Standard Model isn’t a complete picture of the universe—it doesn’t explain gravity, dark matter, or dark energy.. However, by getting a better understanding of it and the Higgs Field, we are one step closer to developing a “Theory of Everything.”

Read more at the Nobel Prize website or the winning work here (Higgs’ 1964 paper) and here (LHC publication).

The STEM Chicksmas Day Five: Quasicrystals

The Stem Chicksmas Chemistry 2011
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For the 12 Days of “The STEM Chicksmas” we’re highlighting 12 scientists who have contributed something innovative and exciting to their field. It is the season of giving, and these brilliant minds have given incredible gifts to the scientific community! This year we’re looking at 12 Nobel Prize winners from the past 15 years in the fields of Physics, Chemistry, and Physiology or Medicine.

Day Five: The 2011 Nobel Prize in Chemistry.

The STEM Chicksmas Nobel Prize 2011 Chemistry
Source: Nobel Prize Summary and Nobel Prize Popular Information

There are two broad types of solids: amorphous and crystalline. In an amorphous solid like quartz or rubber, the molecules are randomly arranged. In a crystalline solid, the atoms are arranged in a pattern that stretches across the entire solid. An example of this is table salt. If you were to look at salt on the atomic level, you would see that each sodium and chloride ion is arranged at a specific distance from each other and in a certain pattern. If you looked in any direction, you would see that this pattern repeats for infinity (or until the edge of the crystal, or if you hit a defect). Up until the 1990s, the requirement for something to be crystalline was for this pattern to be regular and repeating. That means that if you took a small part of the crystal called the unit cell and slid that in any direction, it would superimpose over the atoms there. This is called translational symmetry. Another way of thinking about it is that you can build the crystal up in every direction by attaching the unit cells together at the edge. Crystals can also be classified by their rotational symmetry—that is, how many times you can turn it and still have the same structure.

Only certain degrees of rotational symmetry are possible in crystal lattices: 2, 3, 4, or 6. Degrees of 5 or ones higher than 6 are not allowed. A simple explanation for this is that they cannot be space filling. As an exercise, take a piece of paper and a pen. Try to draw a lattice made up of pentagons that are all the same size. You’ll quickly see that you can’t—there will always be a gap. (Also if you try this, please share the pictures with us!)

So when Dan Shechtman, winner of the 2011 Nobel Prize in Chemistry, discovered a crystal that seemed to have fivefold symmetry in the early 80s, he was stumped. Crystals can have their structures determined by a process called x-ray crystallography. In this process, high intensity light is shined on a crystal. The crystal diffracts the light, and gives a pattern of bright spots that are associated with the structure of the crystal. This “diffraction pattern” can be then analyzed to figure out the shape of the crystal. Shechtman’s diffraction pattern suggested his crystal had five- or tenfold rotational symmetry. He repeated the process a few times, assuming that either his crystal sample was bad or that he was looking at the pattern incorrectly, but each time he got the same result. He eventually published his work and it was very controversial. His supervisor kicked him out of the lab group. He was told to “read a textbook.” Nobel Prize winner Linus Pauling offered him coauthorship on a paper that would contradict his original work by claiming the samples were, in fact, not good enough. (Pauling ended up spending several years trying to explain the problem Shechtman’s crystal presented.)

Eventually Shechtman realized his crystal was not just fivefold symmetric, but icosahedral. An icosahedron is a polygon with 5 triangular faces. The neat thing about icosahedrons is that if you look at them in 6 dimensional space using matrix math, they have transformational symmetry, just like normal crystals! They also found that even though they didn’t have transformational symmetry or long range order in 3D space, there was underlying symmetry. The golden ratio appears over and over again in quasicrystals—the ratio between the distance between two atoms can be represented with the golden ratio. So even while Shechtman’s crystals, which we now call quasicrystals, did not have typical geometric order, they instead had mathematical order. This led to the definition of crystals being changed in 1992 to “any solid having an essentially discrete diffraction diagram.” That means quasicrystals really are crystalline! But we still call the quasicrystals out of convention and because they’re still a little weird.

Shechtman’s discovery is cool for a few different reasons. One, he totally changed the way crystals are considered and shook up the paradigm of the time. Two, he stuck to his theory and believed in his work, even when everyone was telling him he was wrong. Three, quasicrystals have since been discovered in certain types of steel and in a mineral found in a Russian river. Without Shechtman’s work these discoveries would have been overlooked as errors.  The discovery of quasicrystals shows us that sometimes, we can be smarter than the textbook and maybe even a Nobel Prize winner.

Read more at the Nobel Prize website or check out the winning paper here.

The STEM Chicksmas Day Four: Bio Time Travel

The STEM Chicksmas Nobel Prize 2012 Medicine and Physiology
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For the 12 Days of “The STEM Chicksmas” we’re highlighting 12 scientists who have contributed something innovative and exciting to their field. It is the season of giving, and these brilliant minds have given incredible gifts to the scientific community! This year we’re looking at 12 Nobel Prize winners from the past 15 years in the fields of Physics, Chemistry, and Physiology or Medicine.

Day Four: The 2012 Nobel Prize in Medicine or Physiology.

The STEM Chicksmas Nobel Prize 2012 Medicine and Physiology
Source: Nobel Prize Summary and Nobel Prize Popular Information

Can time run backwards? Maybe not, but cell development can, at least according to the 2012 Nobel Laureates in Medicine or Physiology, Sir John B. Gurdon and Shinya Yamanaka. There are three main types of cells in mammals: germ cells (related to reproduction), somatic cells (the flesh and bones of mammals), and stem cells. Stem cells are cells that are not differentiated but are capable of dividing by mitosis. When a cell is differentiated, it makes a new, more specialized cell type. Mitosis is the process by which a cell splits itself into two new identical cells. That means stem cells can not only make more of themselves, they can also differentiate into other types of cells!

There are three types of stem cells: totipotent, pluripotent, and multipotent. An important totipotent cell is the zygote, which is the result of a sperm fertilizing an egg. Totipotent cells can become any type of cell, including those in the amniotic sac and placenta. They differentiate into pluripotent cells, which can become any type of cell except those in the amniotic sac and placenta. Essentially, pluripotent cells give rise to all the cells in an adult, whereas totipotent cells also give rise to those in fetal development. Pluripotent cells differentiate into multipotent cells, which can create cells in certain families. For instance, the hematopoietic stem cell eventually gives rise to blood cells. Pluripotent stem cells are mainly found in embryos. In adults, most stem cells are multipotent. These adult stem cells play important roles in areas such as repairing damaged tissue.

Pluripotent cells are important for research and medicine, because they can be used to make any other type of cell, outside of the amniotic sac and placenta. However, harvesting them from embryos has been historically controversial. But Gurdon and Yamanaka demonstrated that cell development is not a one way street, and they made it possible to get pluripotent cells from adult stem cells. Gurdon made the first “clone” in 1962. He destroyed the nucleus of a frog’s egg and replaced it with an intestinal cell from a tadpole. This cell, with all the genetic information stored in the nucleus, ended up giving rise to tadpoles! This demonstrates two things: one, it’s possible to take the genetic information of a creature and make a new creature of it (the new tadpole was genetically identical to the one the intestinal cell was taken from). The first mammalian clone was the sheep Dolly in the late 90s. Two, it demonstrates that development can run backwards. The intestinal cell he used was already differentiated, yet it still resulted in a whole tadpole. This means that certain conditions experienced by the modified egg cell caused the nucleus of a fully differentiated cell to dedifferentiate to a stem cell and from there differentiate into all other cell types!

Yamanaka was inspired by this work more than 40 years later. He wanted to find out which conditions cause gene expression to induce pluripotency. In Gurdon’s clone, the specialized cell must have made pluripotent cells, but this is only seen by the resulting tadpole. Yamanaka decided to pick apart the process from the inside. He identified the genes associated with pluripotency and injected them into fully differentiated fibroblast cells from mouse skin. Eventually, he narrowed it down to four specific genes responsible for dedifferentiation to pluripotency.

Yamanaka’s induced pluripotent cells were a breakthrough. Scientists all over the world started using his technique to make pluripotent cells in their own labs. There was no longer a need for difficult to obtain embryonic cells when pluripotent cells were now so easy to grow. And like Gurdon demonstrated, the genetic material in these cells could be controlled. Researchers studying diseases can take a cell sample from any patient and make pluripotent stem cells from that. The resulting cell has the patient’s genetic information. This is especially useful for studying hereditary diseases and for looking at genetic predisposition to disease. Research is also being done to look at using pluripotent cells for transplants. A person with diabetes, for example, could receive insulin producing cells instead of having to take insulin injections. Some research also suggests that if the induced pluripotent stem cells cultured from an individual’s own cells, they are not rejected by the body, doing away with the need for immunosuppressants! There is a lot of research still to be done, but it is a promising field for medicine and research.

To read more, check out the Nobel Prize site or the award winning work here (Gurdon) or here (Yamanaka).