Why blueberries won’t turn you blue and other blueberry facts

Blueberries. Credit.


by Adrienne Roehrich, Chemistry Editor

Blueberries in the Northwestern semisphere are the fruit of several shrubs in the genus Vaccinium L.  They grow in all provinces in Canada and all but two of the United States (Nebraska and North Dakota). In the Northwestern semisphere, one can find 43 species of blueberries, depending on the region. Blueberries are found and produced in all hemispheres of the world. However, the species can vary by region.

Taxonomy:
Kingdom: Plantae (Plants)
Subkingdom: Tracheobionta (Vascular plants)
Subdivision: Spermatophyta (Seed plants)
Division: Magnoliophyta (Flowering plants)
Class: Magnoliopsida (Dictyledons)
Subclass: Dilleniidae
Order: Ericales
Family: Ericaceae
Genus: Vaccinium

There are 43 species and 46 accepted taxa overall. Some of the species include fruits we do not necessarily recognize as blueberry, including farkleberry, bilberry, ohelo, cranberry, huckleberry, whortleberry, deer berry, and lingonberry.  (Source

Blueberries are a very popular fruit in the U.S., and is consumed in fresh, frozen, and canned forms. While blueberries are a great fruit to eat to meet your suggested fruit intake, it also is one of the foods that are purported to have properties that it just does not have. This undeserved reputation results from the high levels of anti-oxidants, leading those predisposed to looking for “super foods” to classify blueberries into the anti-oxidant super food category. While eating more healthy foods is always a good idea, no food has curative effects all on its own.

Other aspects of blueberry nutrition includes it as a source of sugar. One cup (148 g) of blueberries contains about 15 g of sugar and 4 g of fiber, a single gram of protein, and half a gram of fat. If you are counting carbs, this cup has 21 g of them. That one cup of blueberries averages about 85 calories, which is approximately the same as a medium apple or orange. While almost all the vitamins and minerals nutrition gurus like to report on are present to some amount, for the 2000-calorie diet, that one cup of blueberries will provide the recommended daily value of 24% of Vitamin C, 36% of Vitamin K, and 25% of manganese. The remaining values range from 0-4%. (Values obtained from Nutrition.com and verified through multiple sources.)

The Wikipedia entry is quite good and well researched (as of August 18, 2012). 

The photo above shows all of the life stages of a blueberry. Berries go from the little red nub at the end of the branch to round and juicy blueberries through fertilization of the ovary, which swells rapidly for about a month, then its growth ceases. The green berry develops with no change in size. The chemicals responsible for the blue color, anthocyanins, begin to turn the berry from green to blue as it develops over about 6 days. The volume of the berry increases during the change in color phase.

Will blueberries turn you blue? In short, no. You can achieve blue skin through the ill-advised practice of drinking silver or you can achieve orangish-yellow skin by eating a large number of carrots. This is because the chemicals causing the skin color are fat soluble and are present in a large quantity in the fat just under the skin, giving the skin those colors. Anthocyanin, the primary chemical causing the blue color in blueberries, is not fat soluble and will not reside in the fat under your skin.

Anthocyanins is a class of over 30 compounds. The chemical structure is generally as shown below. They are polyphenolic, which indicates the 3 ring structures. The “R” indicates different functional groups that change depending on which anthocyanin the structure represents. 


Interestingly, anthocyanins are also pH indicators because their color ranges from yellow to red to blue depending on the local pH. The blue color indicates a neutral pH. The wikipedia page on anthocyanins is also informative (as of August 18, 2012). 

As mentioned before, blueberries are a popular fruit. Recipes abound, but here is one from my own Recipe Codex for Surprise Muffins with blueberries:

Ingredients
  • 6 Tbsp. butter
  • 3/4 cup sugar
  • 2 eggs
  • 1/2 cup milk
  • 1/2 – 1 pint blueberries, fresh or frozen (defrosted)
  • Food coloring, optional
  • 2 cups all-purpose flour
  • 1/4 tsp. salt
  • 1 Tbsp. baking powder
  • Your favorite mini-treat (Hershey’s Kisses, Hugs, Reese’s Mini Cups, strawberry jam, etc.)
Directions
  1. Preheat the oven to 350º. In a large bowl, cream the butter and sugar. You can use a wooden spoon, a potato masher or handheld electric mixer. Mix in the eggs, one at a time, and add the milk.
  2. Rinse the strawberries and cut off the green stem. Mash the berries with a potato masher or puree in a blender. Then stir the berries into the butter and milk mixture. TIP: For muffins with a more blue color, add a few drops of blue food coloring.
  3. In a separate bowl, sift the flour, salt and baking powder. Stir well. Add the flour mixture to the berry mixture. Use a wooden spoon to stir until all the white disappears.
  4. Line the muffin tin with paper liners. Drop the batter from a tablespoon to fill the cups halfway.
  5. Add a surprise: an unwrapped mini treat or 1/2 teaspoon of jam. Then spoon more batter to fill almost to the top.
  6. Bake until the muffins begin to brown and a toothpick inserted near the center (but not in the mini-treat) comes out clean, about 20-25 minutes.
  7. Remove the muffins from the tin and cool.
Or perhaps you are in less of a cooking scientist mood and more in a home lab mood. Try this at-home lab with blueberries about dyes. Adapted from the Journal of Chemical Education.

Items You Need
  • 4 microwavable/stove top staff glasses, pots, or containers at least 1/2 cup in volume
  • tablespoons or 1/4 cup measuring cup
  • water
  • spatula
  • alum (available in the grocery store spice aisle)
  • cream of tartar (available in the grocery store spice aisle)
  • hot pads and tongs
  • at least four small (1-2 in.) squares of white cotton cloth
  • yellow onion skins
  • blueberries
  • spoon
  • paper towels
  • vinegar
  • baking soda
  • a dropper
  • notebook for experimental observations
Procedure
In each step, you will want to record your observations, paying special attention to colors.
  1. Pour 4 tablespoons (1/4 cup) into container 1. Add a pea-sized scoop of alum and about half that amount of cream of tartar and stir. Bring the solution to a boil on the stove top or by microwaving for about 60 seconds. (Your microwave may vary.) Add two small squares of white cotton cloth and boil for two minutes. Set the container aside. The squares will be used in steps 4 and 6.
  2. Tear the outer, papery skin from a yellow onion into pieces no more than 1 inch square. Place enough pieces in a second container to cover its bottom with  2 or 3 layers of onion skin. Add about 4 tablespoons of water to the container. Bring the solution to a boil on the stove top, continuing to boil for 5  minutes.
  3. Wet a new square of cloth with water. Place it in container 2 so it is completely submerged and boil for 1 minute. Using tongs, remove the cloth and rinse it with water. Place the cloth square in the appropriate area on a labeled paper towel.
  4. Use tongs to remove one of the cloth squares from beaker 1. Repeat step 3 using this square. Compare to the dyed cloth square from step 3.
  5. Pour 4 tablespoons of water in a third container. Add 4-5 blueberries to the container and mash them with a spoon. Bring the solution to a boil on the stove, and continue to boil for 5 minutes.
  6. Repeat steps 3 and 4 substituting the blueberry mixture in container 3 for the onion skin mixture in container 2.
  7. Mix a small scoop of baking soda with a tsp of water in a clean container. With a dropper, place 1-2 drops of the baking soda solution in one corner of each cloth square. What happens? Rinse the dropper thoroughly, then place 1-2 drops of vinegar on the opposite corner of each square. What happens? Rinse the fabric squares under cool running water. Is there a change? Allow the squares to dry overnight. Is there any change of the cloth dries?
Optional: Try variations in the procedure such as changing the amount of dye source, the length of time the cloth spends in the dye solution, and the temperature of the dye solution.

Questions to consider
The solution in step 1 is called a mordant. Based on your observations, what is the purpose of a mordant?
Is the dye produced by blueberries really blue? Why might some people not want to wear clothes dyed with blueberries?

———————-
All in all, enjoy your blueberries. As a shrub, it is quite pretty. As a fruit, it is quite yummy. And as the tool in an experiment, it is quite fun.

These views are the opinion of the author and do not necessarily reflect or disagree with those of the DXS editorial team.

Biology Explainer: The big 4 building blocks of life–carbohydrates, fats, proteins, and nucleic acids

The short version
  • The four basic categories of molecules for building life are carbohydrates, lipids, proteins, and nucleic acids.
  • Carbohydrates serve many purposes, from energy to structure to chemical communication, as monomers or polymers.
  • Lipids, which are hydrophobic, also have different purposes, including energy storage, structure, and signaling.
  • Proteins, made of amino acids in up to four structural levels, are involved in just about every process of life.                                                                                                      
  • The nucleic acids DNA and RNA consist of four nucleotide building blocks, and each has different purposes.
The longer version
Life is so diverse and unwieldy, it may surprise you to learn that we can break it down into four basic categories of molecules. Possibly even more implausible is the fact that two of these categories of large molecules themselves break down into a surprisingly small number of building blocks. The proteins that make up all of the living things on this planet and ensure their appropriate structure and smooth function consist of only 20 different kinds of building blocks. Nucleic acids, specifically DNA, are even more basic: only four different kinds of molecules provide the materials to build the countless different genetic codes that translate into all the different walking, swimming, crawling, oozing, and/or photosynthesizing organisms that populate the third rock from the Sun.

                                                  

Big Molecules with Small Building Blocks

The functional groups, assembled into building blocks on backbones of carbon atoms, can be bonded together to yield large molecules that we classify into four basic categories. These molecules, in many different permutations, are the basis for the diversity that we see among living things. They can consist of thousands of atoms, but only a handful of different kinds of atoms form them. It’s like building apartment buildings using a small selection of different materials: bricks, mortar, iron, glass, and wood. Arranged in different ways, these few materials can yield a huge variety of structures.

We encountered functional groups and the SPHONC in Chapter 3. These components form the four categories of molecules of life. These Big Four biological molecules are carbohydrates, lipids, proteins, and nucleic acids. They can have many roles, from giving an organism structure to being involved in one of the millions of processes of living. Let’s meet each category individually and discover the basic roles of each in the structure and function of life.
Carbohydrates

You have met carbohydrates before, whether you know it or not. We refer to them casually as “sugars,” molecules made of carbon, hydrogen, and oxygen. A sugar molecule has a carbon backbone, usually five or six carbons in the ones we’ll discuss here, but it can be as few as three. Sugar molecules can link together in pairs or in chains or branching “trees,” either for structure or energy storage.

When you look on a nutrition label, you’ll see reference to “sugars.” That term includes carbohydrates that provide energy, which we get from breaking the chemical bonds in a sugar called glucose. The “sugars” on a nutrition label also include those that give structure to a plant, which we call fiber. Both are important nutrients for people.

Sugars serve many purposes. They give crunch to the cell walls of a plant or the exoskeleton of a beetle and chemical energy to the marathon runner. When attached to other molecules, like proteins or fats, they aid in communication between cells. But before we get any further into their uses, let’s talk structure.

The sugars we encounter most in basic biology have their five or six carbons linked together in a ring. There’s no need to dive deep into organic chemistry, but there are a couple of essential things to know to interpret the standard representations of these molecules.

Check out the sugars depicted in the figure. The top-left molecule, glucose, has six carbons, which have been numbered. The sugar to its right is the same glucose, with all but one “C” removed. The other five carbons are still there but are inferred using the conventions of organic chemistry: Anywhere there is a corner, there’s a carbon unless otherwise indicated. It might be a good exercise for you to add in a “C” over each corner so that you gain a good understanding of this convention. You should end up adding in five carbon symbols; the sixth is already given because that is conventionally included when it occurs outside of the ring.

On the left is a glucose with all of its carbons indicated. They’re also numbered, which is important to understand now for information that comes later. On the right is the same molecule, glucose, without the carbons indicated (except for the sixth one). Wherever there is a corner, there is a carbon, unless otherwise indicated (as with the oxygen). On the bottom left is ribose, the sugar found in RNA. The sugar on the bottom right is deoxyribose. Note that at carbon 2 (*), the ribose and deoxyribose differ by a single oxygen.

The lower left sugar in the figure is a ribose. In this depiction, the carbons, except the one outside of the ring, have not been drawn in, and they are not numbered. This is the standard way sugars are presented in texts. Can you tell how many carbons there are in this sugar? Count the corners and don’t forget the one that’s already indicated!

If you said “five,” you are right. Ribose is a pentose (pent = five) and happens to be the sugar present in ribonucleic acid, or RNA. Think to yourself what the sugar might be in deoxyribonucleic acid, or DNA. If you thought, deoxyribose, you’d be right.

The fourth sugar given in the figure is a deoxyribose. In organic chemistry, it’s not enough to know that corners indicate carbons. Each carbon also has a specific number, which becomes important in discussions of nucleic acids. Luckily, we get to keep our carbon counting pretty simple in basic biology. To count carbons, you start with the carbon to the right of the non-carbon corner of the molecule. The deoxyribose or ribose always looks to me like a little cupcake with a cherry on top. The “cherry” is an oxygen. To the right of that oxygen, we start counting carbons, so that corner to the right of the “cherry” is the first carbon. Now, keep counting. Here’s a little test: What is hanging down from carbon 2 of the deoxyribose?

If you said a hydrogen (H), you are right! Now, compare the deoxyribose to the ribose. Do you see the difference in what hangs off of the carbon 2 of each sugar? You’ll see that the carbon 2 of ribose has an –OH, rather than an H. The reason the deoxyribose is called that is because the O on the second carbon of the ribose has been removed, leaving a “deoxyed” ribose. This tiny distinction between the sugars used in DNA and RNA is significant enough in biology that we use it to distinguish the two nucleic acids.

In fact, these subtle differences in sugars mean big differences for many biological molecules. Below, you’ll find a couple of ways that apparently small changes in a sugar molecule can mean big changes in what it does. These little changes make the difference between a delicious sugar cookie and the crunchy exoskeleton of a dung beetle.

Sugar and Fuel

A marathon runner keeps fuel on hand in the form of “carbs,” or sugars. These fuels provide the marathoner’s straining body with the energy it needs to keep the muscles pumping. When we take in sugar like this, it often comes in the form of glucose molecules attached together in a polymer called starch. We are especially equipped to start breaking off individual glucose molecules the minute we start chewing on a starch.

Double X Extra: A monomer is a building block (mono = one) and a polymer is a chain of monomers. With a few dozen monomers or building blocks, we get millions of different polymers. That may sound nutty until you think of the infinity of values that can be built using only the numbers 0 through 9 as building blocks or the intricate programming that is done using only a binary code of zeros and ones in different combinations.

Our bodies then can rapidly take the single molecules, or monomers, into cells and crack open the chemical bonds to transform the energy for use. The bonds of a sugar are packed with chemical energy that we capture to build a different kind of energy-containing molecule that our muscles access easily. Most species rely on this process of capturing energy from sugars and transforming it for specific purposes.

Polysaccharides: Fuel and Form

Plants use the Sun’s energy to make their own glucose, and starch is actually a plant’s way of storing up that sugar. Potatoes, for example, are quite good at packing away tons of glucose molecules and are known to dieticians as a “starchy” vegetable. The glucose molecules in starch are packed fairly closely together. A string of sugar molecules bonded together through dehydration synthesis, as they are in starch, is a polymer called a polysaccharide (poly = many; saccharide = sugar). When the monomers of the polysaccharide are released, as when our bodies break them up, the reaction that releases them is called hydrolysis.

Double X Extra: The specific reaction that hooks one monomer to another in a covalent bond is called dehydration synthesis because in making the bond–synthesizing the larger molecule–a molecule of water is removed (dehydration). The reverse is hydrolysis (hydro = water; lysis = breaking), which breaks the covalent bond by the addition of a molecule of water.

Although plants make their own glucose and animals acquire it by eating the plants, animals can also package away the glucose they eat for later use. Animals, including humans, store glucose in a polysaccharide called glycogen, which is more branched than starch. In us, we build this energy reserve primarily in the liver and access it when our glucose levels drop.

Whether starch or glycogen, the glucose molecules that are stored are bonded together so that all of the molecules are oriented the same way. If you view the sixth carbon of the glucose to be a “carbon flag,” you’ll see in the figure that all of the glucose molecules in starch are oriented with their carbon flags on the upper left.

The orientation of monomers of glucose in polysaccharides can make a big difference in the use of the polymer. The glucoses in the molecule on the top are all oriented “up” and form starch. The glucoses in the molecule on the bottom alternate orientation to form cellulose, which is quite different in its function from starch.

Storing up sugars for fuel and using them as fuel isn’t the end of the uses of sugar. In fact, sugars serve as structural molecules in a huge variety of organisms, including fungi, bacteria, plants, and insects.

The primary structural role of a sugar is as a component of the cell wall, giving the organism support against gravity. In plants, the familiar old glucose molecule serves as one building block of the plant cell wall, but with a catch: The molecules are oriented in an alternating up-down fashion. The resulting structural sugar is called cellulose.

That simple difference in orientation means the difference between a polysaccharide as fuel for us and a polysaccharide as structure. Insects take it step further with the polysaccharide that makes up their exoskeleton, or outer shell. Once again, the building block is glucose, arranged as it is in cellulose, in an alternating conformation. But in insects, each glucose has a little extra added on, a chemical group called an N-acetyl group. This addition of a single functional group alters the use of cellulose and turns it into a structural molecule that gives bugs that special crunchy sound when you accidentally…ahem…step on them.

These variations on the simple theme of a basic carbon-ring-as-building-block occur again and again in biological systems. In addition to serving roles in structure and as fuel, sugars also play a role in function. The attachment of subtly different sugar molecules to a protein or a lipid is one way cells communicate chemically with one another in refined, regulated interactions. It’s as though the cells talk with each other using a specialized, sugar-based vocabulary. Typically, cells display these sugary messages to the outside world, making them available to other cells that can recognize the molecular language.

Lipids: The Fatty Trifecta

Starch makes for good, accessible fuel, something that we immediately attack chemically and break up for quick energy. But fats are energy that we are supposed to bank away for a good long time and break out in times of deprivation. Like sugars, fats serve several purposes, including as a dense source of energy and as a universal structural component of cell membranes everywhere.

Fats: the Good, the Bad, the Neutral

Turn again to a nutrition label, and you’ll see a few references to fats, also known as lipids. (Fats are slightly less confusing that sugars in that they have only two names.) The label may break down fats into categories, including trans fats, saturated fats, unsaturated fats, and cholesterol. You may have learned that trans fats are “bad” and that there is good cholesterol and bad cholesterol, but what does it all mean?

Let’s start with what we mean when we say saturated fat. The question is, saturated with what? There is a specific kind of dietary fat call the triglyceride. As its name implies, it has a structural motif in which something is repeated three times. That something is a chain of carbons and hydrogens, hanging off in triplicate from a head made of glycerol, as the figure shows.  Those three carbon-hydrogen chains, or fatty acids, are the “tri” in a triglyceride. Chains like this can be many carbons long.

Double X Extra: We call a fatty acid a fatty acid because it’s got a carboxylic acid attached to a fatty tail. A triglyceride consists of three of these fatty acids attached to a molecule called glycerol. Our dietary fat primarily consists of these triglycerides.

Triglycerides come in several forms. You may recall that carbon can form several different kinds of bonds, including single bonds, as with hydrogen, and double bonds, as with itself. A chain of carbon and hydrogens can have every single available carbon bond taken by a hydrogen in single covalent bond. This scenario of hydrogen saturation yields a saturated fat. The fat is saturated to its fullest with every covalent bond taken by hydrogens single bonded to the carbons.

Saturated fats have predictable characteristics. They lie flat easily and stick to each other, meaning that at room temperature, they form a dense solid. You will realize this if you find a little bit of fat on you to pinch. Does it feel pretty solid? That’s because animal fat is saturated fat. The fat on a steak is also solid at room temperature, and in fact, it takes a pretty high heat to loosen it up enough to become liquid. Animals are not the only organisms that produce saturated fat–avocados and coconuts also are known for their saturated fat content.

The top graphic above depicts a triglyceride with the glycerol, acid, and three hydrocarbon tails. The tails of this saturated fat, with every possible hydrogen space occupied, lie comparatively flat on one another, and this kind of fat is solid at room temperature. The fat on the bottom, however, is unsaturated, with bends or kinks wherever two carbons have double bonded, booting a couple of hydrogens and making this fat unsaturated, or lacking some hydrogens. Because of the space between the bumps, this fat is probably not solid at room temperature, but liquid.

You can probably now guess what an unsaturated fat is–one that has one or more hydrogens missing. Instead of single bonding with hydrogens at every available space, two or more carbons in an unsaturated fat chain will form a double bond with carbon, leaving no space for a hydrogen. Because some carbons in the chain share two pairs of electrons, they physically draw closer to one another than they do in a single bond. This tighter bonding result in a “kink” in the fatty acid chain.

In a fat with these kinks, the three fatty acids don’t lie as densely packed with each other as they do in a saturated fat. The kinks leave spaces between them. Thus, unsaturated fats are less dense than saturated fats and often will be liquid at room temperature. A good example of a liquid unsaturated fat at room temperature is canola oil.

A few decades ago, food scientists discovered that unsaturated fats could be resaturated or hydrogenated to behave more like saturated fats and have a longer shelf life. The process of hydrogenation–adding in hydrogens–yields trans fat. This kind of processed fat is now frowned upon and is being removed from many foods because of its associations with adverse health effects. If you check a food label and it lists among the ingredients “partially hydrogenated” oils, that can mean that the food contains trans fat.

Double X Extra: A triglyceride can have up to three different fatty acids attached to it. Canola oil, for example, consists primarily of oleic acid, linoleic acid, and linolenic acid, all of which are unsaturated fatty acids with 18 carbons in their chains.

Why do we take in fat anyway? Fat is a necessary nutrient for everything from our nervous systems to our circulatory health. It also, under appropriate conditions, is an excellent way to store up densely packaged energy for the times when stores are running low. We really can’t live very well without it.

Phospholipids: An Abundant Fat

You may have heard that oil and water don’t mix, and indeed, it is something you can observe for yourself. Drop a pat of butter–pure saturated fat–into a bowl of water and watch it just sit there. Even if you try mixing it with a spoon, it will just sit there. Now, drop a spoon of salt into the water and stir it a bit. The salt seems to vanish. You’ve just illustrated the difference between a water-fearing (hydrophobic) and a water-loving (hydrophilic) substance.

Generally speaking, compounds that have an unequal sharing of electrons (like ions or anything with a covalent bond between oxygen and hydrogen or nitrogen and hydrogen) will be hydrophilic. The reason is that a charge or an unequal electron sharing gives the molecule polarity that allows it to interact with water through hydrogen bonds. A fat, however, consists largely of hydrogen and carbon in those long chains. Carbon and hydrogen have roughly equivalent electronegativities, and their electron-sharing relationship is relatively nonpolar. Fat, lacking in polarity, doesn’t interact with water. As the butter demonstrated, it just sits there.

There is one exception to that little maxim about fat and water, and that exception is the phospholipid. This lipid has a special structure that makes it just right for the job it does: forming the membranes of cells. A phospholipid consists of a polar phosphate head–P and O don’t share equally–and a couple of nonpolar hydrocarbon tails, as the figure shows. If you look at the figure, you’ll see that one of the two tails has a little kick in it, thanks to a double bond between the two carbons there.

Phospholipids form a double layer and are the major structural components of cell membranes. Their bend, or kick, in one of the hydrocarbon tails helps ensure fluidity of the cell membrane. The molecules are bipolar, with hydrophilic heads for interacting with the internal and external watery environments of the cell and hydrophobic tails that help cell membranes behave as general security guards.

The kick and the bipolar (hydrophobic and hydrophilic) nature of the phospholipid make it the perfect molecule for building a cell membrane. A cell needs a watery outside to survive. It also needs a watery inside to survive. Thus, it must face the inside and outside worlds with something that interacts well with water. But it also must protect itself against unwanted intruders, providing a barrier that keeps unwanted things out and keeps necessary molecules in.

Phospholipids achieve it all. They assemble into a double layer around a cell but orient to allow interaction with the watery external and internal environments. On the layer facing the inside of the cell, the phospholipids orient their polar, hydrophilic heads to the watery inner environment and their tails away from it. On the layer to the outside of the cell, they do the same.
As the figure shows, the result is a double layer of phospholipids with each layer facing a polar, hydrophilic head to the watery environments. The tails of each layer face one another. They form a hydrophobic, fatty moat around a cell that serves as a general gatekeeper, much in the way that your skin does for you. Charged particles cannot simply slip across this fatty moat because they can’t interact with it. And to keep the fat fluid, one tail of each phospholipid has that little kick, giving the cell membrane a fluid, liquidy flow and keeping it from being solid and unforgiving at temperatures in which cells thrive.

Steroids: Here to Pump You Up?

Our final molecule in the lipid fatty trifecta is cholesterol. As you may have heard, there are a few different kinds of cholesterol, some of which we consider to be “good” and some of which is “bad.” The good cholesterol, high-density lipoprotein, or HDL, in part helps us out because it removes the bad cholesterol, low-density lipoprotein or LDL, from our blood. The presence of LDL is associated with inflammation of the lining of the blood vessels, which can lead to a variety of health problems.

But cholesterol has some other reasons for existing. One of its roles is in the maintenance of cell membrane fluidity. Cholesterol is inserted throughout the lipid bilayer and serves as a block to the fatty tails that might otherwise stick together and become a bit too solid.

Cholesterol’s other starring role as a lipid is as the starting molecule for a class of hormones we called steroids or steroid hormones. With a few snips here and additions there, cholesterol can be changed into the steroid hormones progesterone, testosterone, or estrogen. These molecules look quite similar, but they play very different roles in organisms. Testosterone, for example, generally masculinizes vertebrates (animals with backbones), while progesterone and estrogen play a role in regulating the ovulatory cycle.

Double X Extra: A hormone is a blood-borne signaling molecule. It can be lipid based, like testosterone, or short protein, like insulin.

Proteins

As you progress through learning biology, one thing will become more and more clear: Most cells function primarily as protein factories. It may surprise you to learn that proteins, which we often talk about in terms of food intake, are the fundamental molecule of many of life’s processes. Enzymes, for example, form a single broad category of proteins, but there are millions of them, each one governing a small step in the molecular pathways that are required for living.

Levels of Structure

Amino acids are the building blocks of proteins. A few amino acids strung together is called a peptide, while many many peptides linked together form a polypeptide. When many amino acids strung together interact with each other to form a properly folded molecule, we call that molecule a protein.

For a string of amino acids to ultimately fold up into an active protein, they must first be assembled in the correct order. The code for their assembly lies in the DNA, but once that code has been read and the amino acid chain built, we call that simple, unfolded chain the primary structure of the protein.

This chain can consist of hundreds of amino acids that interact all along the sequence. Some amino acids are hydrophobic and some are hydrophilic. In this context, like interacts best with like, so the hydrophobic amino acids will interact with one another, and the hydrophilic amino acids will interact together. As these contacts occur along the string of molecules, different conformations will arise in different parts of the chain. We call these different conformations along the amino acid chain the protein’s secondary structure.

Once those interactions have occurred, the protein can fold into its final, or tertiary structure and be ready to serve as an active participant in cellular processes. To achieve the tertiary structure, the amino acid chain’s secondary interactions must usually be ongoing, and the pH, temperature, and salt balance must be just right to facilitate the folding. This tertiary folding takes place through interactions of the secondary structures along the different parts of the amino acid chain.

The final product is a properly folded protein. If we could see it with the naked eye, it might look a lot like a wadded up string of pearls, but that “wadded up” look is misleading. Protein folding is a carefully regulated process that is determined at its core by the amino acids in the chain: their hydrophobicity and hydrophilicity and how they interact together.

In many instances, however, a complete protein consists of more than one amino acid chain, and the complete protein has two or more interacting strings of amino acids. A good example is hemoglobin in red blood cells. Its job is to grab oxygen and deliver it to the body’s tissues. A complete hemoglobin protein consists of four separate amino acid chains all properly folded into their tertiary structures and interacting as a single unit. In cases like this involving two or more interacting amino acid chains, we say that the final protein has a quaternary structure. Some proteins can consist of as many as a dozen interacting chains, behaving as a single protein unit.

A Plethora of Purposes

What does a protein do? Let us count the ways. Really, that’s almost impossible because proteins do just about everything. Some of them tag things. Some of them destroy things. Some of them protect. Some mark cells as “self.” Some serve as structural materials, while others are highways or motors. They aid in communication, they operate as signaling molecules, they transfer molecules and cut them up, they interact with each other in complex, interrelated pathways to build things up and break things down. They regulate genes and package DNA, and they regulate and package each other.

As described above, proteins are the final folded arrangement of a string of amino acids. One way we obtain these building blocks for the millions of proteins our bodies make is through our diet. You may hear about foods that are high in protein or people eating high-protein diets to build muscle. When we take in those proteins, we can break them apart and use the amino acids that make them up to build proteins of our own.

Nucleic Acids

How does a cell know which proteins to make? It has a code for building them, one that is especially guarded in a cellular vault in our cells called the nucleus. This code is deoxyribonucleic acid, or DNA. The cell makes a copy of this code and send it out to specialized structures that read it and build proteins based on what they read. As with any code, a typo–a mutation–can result in a message that doesn’t make as much sense. When the code gets changed, sometimes, the protein that the cell builds using that code will be changed, too.

Biohazard!The names associated with nucleic acids can be confusing because they all start with nucle-. It may seem obvious or easy now, but a brain freeze on a test could mix you up. You need to fix in your mind that the shorter term (10 letters, four syllables), nucleotide, refers to the smaller molecule, the three-part building block. The longer term (12 characters, including the space, and five syllables), nucleic acid, which is inherent in the names DNA and RNA, designates the big, long molecule.

DNA vs. RNA: A Matter of Structure

DNA and its nucleic acid cousin, ribonucleic acid, or RNA, are both made of the same kinds of building blocks. These building blocks are called nucleotides. Each nucleotide consists of three parts: a sugar (ribose for RNA and deoxyribose for DNA), a phosphate, and a nitrogenous base. In DNA, every nucleotide has identical sugars and phosphates, and in RNA, the sugar and phosphate are also the same for every nucleotide.

So what’s different? The nitrogenous bases. DNA has a set of four to use as its coding alphabet. These are the purines, adenine and guanine, and the pyrimidines, thymine and cytosine. The nucleotides are abbreviated by their initial letters as A, G, T, and C. From variations in the arrangement and number of these four molecules, all of the diversity of life arises. Just four different types of the nucleotide building blocks, and we have you, bacteria, wombats, and blue whales.

RNA is also basic at its core, consisting of only four different nucleotides. In fact, it uses three of the same nitrogenous bases as DNA–A, G, and C–but it substitutes a base called uracil (U) where DNA uses thymine. Uracil is a pyrimidine.

DNA vs. RNA: Function Wars

An interesting thing about the nitrogenous bases of the nucleotides is that they pair with each other, using hydrogen bonds, in a predictable way. An adenine will almost always bond with a thymine in DNA or a uracil in RNA, and cytosine and guanine will almost always bond with each other. This pairing capacity allows the cell to use a sequence of DNA and build either a new DNA sequence, using the old one as a template, or build an RNA sequence to make a copy of the DNA.

These two different uses of A-T/U and C-G base pairing serve two different purposes. DNA is copied into DNA usually when a cell is preparing to divide and needs two complete sets of DNA for the new cells. DNA is copied into RNA when the cell needs to send the code out of the vault so proteins can be built. The DNA stays safely where it belongs.

RNA is really a nucleic acid jack-of-all-trades. It not only serves as the copy of the DNA but also is the main component of the two types of cellular workers that read that copy and build proteins from it. At one point in this process, the three types of RNA come together in protein assembly to make sure the job is done right.


 By Emily Willingham, DXS managing editor 
This material originally appeared in similar form in Emily Willingham’s Complete Idiot’s Guide to College Biology

How chili powder can kill



Source. Credit.

How can chili powder kill a child? Dr. Rubidium explains.
by Dr. Rubidium, Ph.D., DXS contributor

On the evening of Sunday, January 6th, 2-year-old Joileen G. was pronounced dead at a San Bernardino hospital. A few hours into Monday, Joileen’s caregiver for that Sunday — Amanda Sorensen — was arrested. On Wednesday, Ms. Sorensen, who is also the girlfriend of Joileen’s father, was charged with “…malice aforethought murder…” and “…assault… by means of force that to a reasonable person would be likely to produce bodily injury, resulting in the child’s death.” The alleged “means of force” wasn’t a belt or a fist, but chili powder.

Though it will likely take weeks before the exact cause and manner of death are known from an autopsy and toxicology tests, various media outlets are reporting that Joileen died of “chili powder poisoning.”

Millions to billions of people enjoy chili peppers world-wide each day, from eating handfuls of whole chili peppers to a few shakes of hot sauce on their eggs. Chili peppers and their products aren’t considered a poison, but that’s because most of us have far too narrow a view of poisons. The field of poisons is actually very broad, as are its definitions. 

For example, for toxicologists, a poison is any substance that is harmful when administered to a living organism. But quantity (dose) and species (you versus, say, a turtle) and route (mouth? skin?) and what it’s combined with count, too. Other factors influencing whether or not something will poison you include age, sex, health, and genetics

In other words, almost anything can be a poison at the right (or wrong Continue reading

Is there glamour in science? There are certainly no scientists in Glamour

Hedy Lamarr: actress, pinup “girl,” and, oh, yeah,  inventor.

Is there glamour in science?

The answer to that question depends on what you mean by “glamour.” Do we get to dress up in clicky heels and walk red carpets? Well, we can do the heels, sure, but red carpets aren’t a frequent feature in the life of most scientists, unless you count that horrible red patterned stuff conference hotels seem to like so much.

Do we travel the world? Sure–see “conference” in previous paragraph. Our conferences can take us to places we never might have gone were it not for our abiding interest in stars or fruit flies or the finer points of protein signaling. If you’re the kind of scientist who does field work with hyenas or needs samples from Antarctica, then your travel can be even more exotic. Do we, like actresses or singers or Kim Kardashian, get to spend our days doing what we love, bringing IT to the world? Hell, yes, we do.

Heels (optional), travel to far-flung locations, passion for what we do, bringing IT. Yep…there’s some glamour in science. And you know what? I’d hazard that while we’re doing it, we’re feeling “beyond empowered.”

The reason I ask is that Glamour magazine just release its “Women of the Year” awards. Before I talk about recipients–or non-recipients–I would like to review the magazine’s mission statement:

Glamour is a magazine that translates style and trends for the real lives of women. Our award-winning editorial covers the most pressing interests of our 12.4 million readers: from beauty, fashion and health to politics, Hollywood and relationships. We’re often optimistic, always inclusive, beyond empowering and can always separate the Dos from the Don’ts. Our readers live for fashion, live for beauty and most of all, live for Glamour.

You’ll see that they seek to cover the “most pressing interests” of their readers, that they are “always inclusive” and “beyond empowering,” and that their readers live for, among other things, beauty and Glamour. I am going to pretend that wedged in there, tacit but present, between “health” and “politics” is “science.” Why? Because nothing but science can bring you solid information about your health. Because politics have a powerful influence over how that science can be used for your health. And because if you live for beauty, science can bring you beauty that takes your breath away, like this:

A stellar nursery in our intergalactic neighborhood.

And this:
Scanning electron microsope image of the lower surface of a leaf from a black walnut tree.

Scientists are the explorers, the discovers, and the investigators…and sometimes, their work becomes art.

Given that science can be so glamorous, so beautiful, so empowering, you might think that the editors of Glamour, which offers its readers all three, might have included a scientist in its “Women of the Year” awards.

They did not. 

That is not to diminish the fabulous, empowered women they did include. Gloria Steinem? Check. Gabrielle Giffords? Oh, yes. The beautiful, gutsy, empowered Esraa Abdel Fattah? Yes, and thank you. Arianna Huffington’s there…although I find what her HuffPo Website countenances for health–including women’s health–sometimes less than empowering. There’s an artist, there’s a fashion designer, there’s…um…Laura Bush and her daughters and…J. Lo. Lea Michelle, a grown woman and another Woman of the Year, is depicted chirpily exclaiming that “I would be happy to be a high school student forever.”

It’s a mixed bag. But in that bag, search as you will, you will find no scientists. Women who live glamorous lives, traveling, engaging, empowered and empowering. Women like Mireya Mayor, who despite her walking the walk in Pink Boots and a Machete, despite identifying a new species of lemur (video), despite her high-profile as an explorer and on television, does not fit the bill for Glamour.


One reason you find no scientists is that Glamour doesn’t seem to have a “Woman of the Year” category that includes science. They’ve selected some women who truly are inspirations, some that make you think, “Whuh?” (Kim Kardashian as “Entrepreneur of the Year” for UK Glamour comes to mind), and even some girls. Kardashians not withstanding, when Amy Poehler makes a list like this, you’ve got to give the editors some credit. 

So, I ask. Can the editors at Glamour give women in science some credit, too? Women like Elodie Ghedin, 2011 Macarthur Fellow and virologist whose work directly addresses critical public health issues? Or Ada Yonath, who was awarded the 2009 Nobel Prize in Chemistry for working on that tiniest of cellular structures, the ribosome? Or Elizabeth Blackburn or Carol W. Greider, who received the Nobel Prize in Physiology or Medicine in 2009 for their work in unlocking some of the secrets to aging? Or Susan Niebur, former NASA astrophysicist and four-time breast cancer survivor who has worked tirelessly while fighting inflammatory breast cancer to promote breast cancer research, awareness of inflammatory breast cancer (the cancer that kills without a lump), science outreach, and women in science?

Glamour editors…women need science and girls and women need inspiration from scientists. Your list of “Women of the Year” includes women who are enormously inspirational and who have done immeasurable good for women. For 2012, please consider that women scientists fit that definition, too, and can also bring the glamour of passion and empowerment to your readers. Those 12.4 million women will thank you.

By Emily Willingham

Backyard Brains: Affordable neuroscience

Mouse neurons. Image via Wikimedia Commons.
Originally published in PLoS Biology.

Nerve cells, called neurons, are special cells. They interact with each other and with other tissues in part by using electrical impulses. The cool thing about these cells is that thanks to their electrical signaling, we can measure when they’re sending their messages. A neuroscientist friend of mine once poetically described as “exquisite” the ability to measure the firing of a single neuron in a finch brain. There is something special about being able to observe that usually hidden process of signaling that underlies every move you make, every thought you have, and every sensation you detect.

The very word “neuroscience” sounds expensive. Measuring the signaling of nerves? That sounds pretty fancy. But with some wires and basic neuroscience tools, anyone can give it a try, measuring the nerve signaling, for example, in an insect. Which, do you think, would be the more memorable learning experience, a full-on sensory exposure to the sights and sounds of neuron signaling, or this? 


Now, a company called Backyard Brains is really bringing the neuroscience to the people. You don’t have to use their affordable kits in your backyard, but as neuroscientist and writer Mo Costandi highlights today in an interview with Tim Marzullo, co-founder of Backyard Brains, this level of technology can become available to high-school students anywhere. In the interview, Marzullo notes that the goal is to produce kits that lower the fiscal and resource requirements for making neuroscience available to people who aren’t graduate students in neuroscience.

As part of their bringing the neuroscience to the people, the Backyard Brains scientists have created the Spiker Box kit, which lets students listen to neurons firing in a de-legged cockroach. These kits are friendly with computers, iPhones, and iPads, so students can use these devices to record and listen to the Zzzzzzztt! of a firing neuron (see video below). Electrophysiology in action, made accessible. 


An even fancier introduction to science awaits. Some proteins are especially made to change their shape in response to a light trigger. Scientists have produced animals–mostly fruit flies–that make these proteins in some neurons, where they don’t usually occur. With light-reactive proteins present in the neurons, researchers can actually make the neurons fire by giving them a shot of laser light. In other words, they can make the animals move using light. Wouldn’t it be cool if classroom students could see that kind of neuroscience in action?

Backyard Brains is on the case. They’re working on a product that will allow students to use blue light emitted from an iPad to trigger light-reactive proteins in nerves that communicate with muscle cells. Because the process involves light and organisms with introduced genes, it’s called optogenetics. That sounds even more swanky than neuroscience, but Backyard Brains is working on making it accessible.

Other Backyard Brains products include RoboRoach (you’ll have to read that one for yourself), soldering kits, and the roaches themselves

Emily Willingham

As Seen on TV! Age Your Wine in 10 Seconds!!!!

Old, old wine. (Source)

Anyone who watches TV, reads magazines, or flips through catalogs has seen some interesting products. Maybe they seem plausible to you, maybe they don’t. However, a little investigation shows they are based less on science and well…actually working, and more on wishful thinking. At worst they’re actual con-jobs, designed to separate you from your money as efficiently as possible (which I guess is a certain standard of success).


As a result, we at Double X Science are starting a new series: “As Seen on TV!” In these features, we’ll look at some of the products shilled on talk shows and infomercials, items lurking between the articles you read in magazines, or things you might find on the shelves of the stores where you shop.

Our first entry is one I spotted in SkyMall, the catalog you (if you’re like me) read if you forget to bring a book on an airplane. Where else can you find dog water bowls shaped like toilets or sports chairs built deliberately too large for anyone, so you look tiny sitting in them? While the catalog is full of impractical items (to put it mildly), some of them go beyond that into the realm of…imagination. Yeah, I’ll call it that. It avoids potential lawsuits.

It’s the Aging Accelerator! With Magnets!

Here’s the idea: depending on which device you buy, you insert either a glass or a bottle of wine, and within 10 seconds! it ages the wine, with the unspoken assumption that this is desirable. (It also evidently works for whiskey, but I’ll skip that discussion in the current article.) Now, anything that promises to drastically alter something within 10 seconds! is probably suspicious to begin with, but that’s the part I’m going to leave alone. After all, magnets do work quickly, so if the device does what it claims to do, it’s quite possible that 10 seconds will be enough time for the magic to happen.

Well, it seems like magic to me. I went to a winery last weekend, and spoke to one of the vintners there (yup, that’s the name for ‘em). She told me that not all wines should be aged, and the reason has to do both with the way wine is made and how it is stored.

First, not all wine should be aged! All wines actually go bad over time, including many of the usual types you may see in the store. That time may be pretty long, but you don’t want to just buy any bottle, stick it in your basement, and wait 20 years to drink it – most of them won’t taste good. According to my source, the days are gone where you might buy bottles of wine and put them in a cellar for your children. (Who has a wine cellar now anyway? I live in a second-floor apartment!) Basically, my source tells me to ask an expert if you have any doubts, but basically all wine is sold today in a drinkable state – no aging is necessary or even wanted. (I can’t endorse it, but Wikipedia has a list of wines that can be aged, and possible ranges.) Earth’s magnetic field has nothing to do with the aging process, whatever the ad says.

Second, the reason some wines age better than others has to do with their chemistry: how much sugar is in the grapes and how much tannin content they have. Red wines typically are higher in tannins because the skins are thrown in with the flesh of the fruit – and tannins act as a preservative. Sugar also acts as a preservative, but it’s not as effective, so white wines (lower in tannins, higher in sugar) don’t keep as well.

The point I’m trying to make is that wine aging isn’t mysterious, either why it happens or how. I don’t have the “Aging Accelerator” package in front of me, so I can’t tell you if they give advice on which wines to put in it and which ones to avoid, but the picture shows both reds and whites. So let’s turn to the way the device is supposed to work: magnetism.

They certainly have one thing right: neodymium magnets are very strong! (Neodymium is one of the “rare earth” elements, found near the bottom of the periodic table, so sometimes you’ll see them referred to as “rare earth magnets”.) When I’ve used neodymium magnets for various experiments, two of them attracting each other pinched my fingers hard enough to create blood blisters.

Admittedly magnets can seem mysterious: understanding exactly how they work requires looking at electrons and atoms, which might seem a little out of the ordinary. However, challenging isn’t the same thing as magical, but some people seem to think that magnets are capable of all sorts of feats, from curing arthritis to – yes – aging wine.

How magnets actually work could be the topic of an “Everyday Science” post, but in brief: the way a material responds to a magnet is called its magnetic susceptibility. Some materials, like neodymium, are very susceptible, but most things aren’t, including the human body. (Some organisms such as pigeons use Earth’s magnetic field to navigate, but exactly how they do it is still not known.) I couldn’t find any particular data on the magnetic susceptibility of tannins or other molecules in wine, but my feeling is it’s not large. Tannins are big biological molecules – think DNA or proteins – and those don’t tend to be magnetic.

But here’s the deal: suppose tannins are magnetic. Why then would exposing them to a magnetic field age the wine? Simply putting a strong magnet near your wine would merely rearrange the molecules inside the liquid – it’s like stirring it, in other words. Obviously stirring something can change the way it tastes, since it can mix sediments in, but that’s not the same thing as aging.

So, let’s wrap up: why should we be suspicious of paying $60 or $100 for an “Aging Accelerator”?
  • The concept misuses a well-understood physical principle – magnetism. Just because someone doesn’t understand how it works doesn’t mean it can perform miracles.
  • The aging process is chemical, and we understand how that works – it involves tannins, sugars, and other molecules. There are no secrets, in other words, and nothing simple to make your wine taste better.
  • Basically, if it sounds like a magic trick, it probably is – but its main result will be to magic money out of your pocket.
We’ll see these kinds of rules repeated throughout the series!

Stay tuned for further installments of “As Seen on TV!”


By DXS Physics Editor Matthew Francis 




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