Archive for the ‘chemistry’ Category

A friend and I met for an afternoon chat; we saw one another in the parking lot and together headed toward our destination. We talked as we walked, slowly tracing our way to the awaiting patio. At some point along our journey, we simultaneously noticed that we had begun to drift apart. We exchanged a look and each of us gazed down, both wondering what had caused us to subconsciously choose different paths. Interestingly, she had unwittingly followed a curvy sidewalk carved into the landscaped lawn. I, on the other hand, had continued to march straight toward the destination, inadvertently pursuing the shortest distance between two points.

We giggled, as girls do, sparking a lively discussion regarding our innate differences – which, of course, resulted in an appreciation of our overall similarities. I realized the acquaintances who become my close friends mimic the phenomenon we experienced while walking: They are the people who confidently and independently follow their own path, yet arrive at the same destination. (I’m certain there’s an Ayn Rand quote in here somewhere.)

We do what we do. And we do what we want. (Caveat: What some people want is to do what they think others want them to do, or expect them to do.) But why is this? Are mere chemicals responsible for free will? What pathways give us individuality, from whence stems innate motivation (or lack thereof); can a change in chemicals change innate responses? Are our subconscious decisions predetermined? Are they dynamic in space, time, and circumstance? Can we purposely choose against them? Are we able to permanently alter our seemingly inherent characteristics?

I could go on and on with these questions; unfortunately, not I nor anyone else really has an answer. We have many clues, glimpses, hopes; but alas, nothing concrete, nothing that holds true uniformly or ubiquitously for the entire human population. Interestingly, while there are many drugs that affect personality, decision-making, and preference, these compounds are often among the least understood; in fact, the mechanisms of action for entire classes of mood-altering substances remain wholly elusive. Doctors prescribe anti-depressants based solely upon the appearance of effectiveness, with no understanding whatsoever of how or why they work. There do seem to be some consistent biochemical messengers that pop up again and again in studies of personality, attitude, choice, inclination, and other cognitive-based traits; these compounds are inevitably influenced by the drugs we find effective at eliciting responses in these areas (though, oddly, often we only notice this ex post facto).

I’m enthralled by these compounds. Not only are their direct effects (those we’ve discovered so far, anyway) amazing, but there seems no bodily pathway immune from some indirect effect of their action. They serve as a dynamic reminder that our bodies run not on a series of one-way linear biochemical reactions, but that we function as a network of interconnected, amenable reactions – and because the whole is greater than the sum of its parts, even the most innocuous compounds are vital to our optimal functioning.

Monoamine neurotransmitters appear to play an important role in linking our conscious behaviors with our subconscious existence. These include the lately in vogue compounds serotonin, dopamine, norepinephrine, and their relatives. Just knowing which compounds are involved seems only the tip of the iceberg, however: Not only does the manufacture, quantity, location, and concentration of the chemical in question matter, but so does the characteristics of the corresponding receptor proteins as well as their ratios and interactions with seemingly unrelated pathways along the route. It seems that dopamine, in particular, has a functional role in our decision-making processes, all of which probably have a subconscious component.

Do yourself a google for the hypothalamic–pituitary–adrenal (HPA) axis and read all about how our major body systems are intertwined and interdependent. I especially enjoy learning about how my gut has a mind of its own – complete with literal mood swings and impressionable responses to my bodily conditions and those substances I choose to expose my innards to.

Fascinatingly, these compounds that make us individuals also seem to play a role in social interactions and cohesion. I am currently reading The Wisdom of Crowds, given to me by a former student (and ongoing friend); I cannot help but suspect maybe culture is actually the average of our individuality, beautiful and wondrous exactly by its projection of the best of our collective biochemical tendencies, exactly capturing the perfection of our imperfections.

Tonicity

Posted: February 10, 2011 in chemistry

So the concept of tonicity refers to a comparison between two solutions. It is not a type of chemical reaction, nor does it make sense all on its own.

When you are looking at two different substances, you may compare them if you want to know various properties, such as which way diffusion will occur between them. If they are separated by a semi-permeable membrane, the diffusion which takes place will potentially be only that of water – termed osmosis. So in biology, when we ask about tonicity we may really be asking about osmotic pressure (see handout from this week’s lab; it can also be found in our Campus Cruiser lecture page “Shared Files” under “Handouts” as “Crossing the Membrane” – online in color it may be more help than printed in black and white).

What did I just say??

Let’s boil it down (pun intended…): Wikipedia says this about tonicity. Once again, I officially denounce Wikipedia!! Whew, now that that’s out of the way, I totally suggest you read the Wikipedia entry for tonicity 🙂 I also suggest you supplement this brief tidbit of knowledge with the information provided here.

Additionally, this website cracks me up. I mean, really. I am a fairly extreme nerd, but a website with this name? I feel better about myself already. And you will not only laugh but also learn from it. Whoa!

At this point I encourage you to revisit (or just look up) the concept of dynamic equilibrium. I think you may find a good ideological fit here.

When we say that something is hypertonic to something else, it means that particular substance has a higher concentration of dissolved solute particles than the object of comparison. On the other hand, when we say that something is hypotonic to something else, it means that substance has a relatively lower concentration of dissolved molecules within the solvent. When two substances are isotonic, the solutions have equal (relative) concentrations of solute and solvent.

None of these terms imply a chemical reaction has taken place, as diffusion and osmosis occur in absence of energy release or gain. It is merely a balancing act – fulfillment of the laws of thermodynamics, which take place in absence, and without regard to, living systems.

Here are some useful videos:

Hydrophobia

Posted: February 9, 2011 in biochemistry, chemistry

Fat is all the rage: From dissing trans to flaunting omega-3s, everyone who is anyone is talking about it. But what has made fat so phat?

Lipids are composed of hydrocarbons and are insoluble (or have limited solubility) in water. This category of organic molecule includes a relatively diverse range of compounds, including waxes, terpenes, steroids, oils, and, yes, those things we call fats. In addition, “fat-soluble” vitamins (A, D, E, and K) are themselves lipids. This is why you are told to add fat to your salad – since they won’t dissolve in water you don’t get these nutrients unless you emulsify them!

A primary role for lipids is maintaining a barrier between the hydrophilic and homeostatic internal cell environment and dynamic external conditions. Phospholipids play the role of protective barrier, forming that selectively, semi-permeable plasma membrane around our cells. Cholesterol is a lipid steroid that is a CRUCIAL cell membrane component, buffering us against temperature and providing other unique functions. We’ll talk more about that later.

In addition to being major cell membrane components, lipids are essential for cellular signaling (e.g. hormones), immune function, and serve as our long-term energy storage molecules (you already know this, though probably in less-politically-correct terminology…). Fat is more efficient than other macromolecules at storing potential energy (as trapped in the chemical bonds), holding 9 kcal of chemical potential energy per gram.

Fats and oils are composed of the three-carbon alcohol glycerol attached to one, two, or three fatty acid chains. When all three of the glycerol carbons are condensed with a fatty acid “tail,” we know the resulting molecule as a triglyceride.

Hydrocarbon chains can be saturated or unsaturated. Saturation just means that all the carbon atoms have four (their maximum!) single bonds, while the degree of unsaturation corresponds to the number of double bonds introduced between carbon atoms. Since the general definition of “saturation” implies being filled or full, it makes sense to conceptualize that the chemical bonding capacity is fully utilized in saturated compounds.

Notice how the double bonds produce “kinks” in the chain? As it turns out, the level of unsaturation corresponds to the fluidity of the fat. That’s why saturated fats are solid at room temperature, while polyunsaturated fats tend to be fluid. “Trans” fats are artificially (usually) produced double bonds (“hydrogenation” is the chemical process of introducing trans-double bonds to a fatty acid chain – watch out for this sneaky label terminology); however, they fail to produce the characteristic kinks in fatty acid chains. The maintenance of a rigid (straight) structure allows for a more solid form and gives us margarine and shortening. However, your body isn’t fooled by this fake stuff and we now know it was a really, really bad idea…

What else is a bad idea? Taking anabolic steroids. Well, okay, that is purely opinion and doesn’t always hold true but you see my point. Which is to transition into talk about the steroid class of lipids. All steroid compounds have a characteristic carbon backbone of a fused, four-ring structure on which various functional groups are attached.

Cholesterol, a good guy, is synthesized by our bodies (no dietary input needed!) and, in addition to serving as a crucial membrane component, also serves as a precursor to sex hormones and Vitamin D (a conversion pathway activated by unfiltered sunlight!). The way your body transports insoluble things like cholesterol from cell to cell, through your bloodstream for instance, is by packing them up inside spherical carrier molecules…

Lipoproteins are globs of protein and lipids all intertwined. These are categorized according to density. Since fat is less dense than protein (think: fat floats, meat sinks), lower density lipoproteins are those that have a relatively high proportion of fat to protein. On the other hand, higher density lipoproteins have a higher ratio of protein to fat. But wait a second! Do those terms sound vaguely familiar? I hope so! Low-density lipoprotein and high-density lipoprotein are also know as LDL and HDL, respectively. Cholesterol is cholesterol; but to be healthy we need protein-packed HDL delivering it to all the right places. LDL is not so efficient at distribution, and also tends to accumulate in the body’s passageways.

Okay now to the really hot topic. The term omega, as it relates to fatty acids, refers to the terminal carbon atom farthest from the functional acidic (carboxyl) group. In other words, polyunsaturated fatty acids have two distinctive “sides,” or endings. On one side is an acidic carboxyl group (let’s call this the “alpha” end), while on the other side lies an “omega” end. The number associated with a type of fat defines the position of the first double bond (unsaturation) relative to the omega end. For example, omega-6 fatty acids have a double bond on the sixth carbon atom from the omega side.

There are three major classes of omega fats that are important in our diet. These are omega-3s, omega-6s, and omega-9s. All three serve functional physiological roles, and it seems fairly meaningless to discuss the requirements for each individually. What seems relevant and important to our health is the RATIO of each in our bodies. It appears optimal to have relatively high levels of omega-3s, medium levels of omega-6s, and low levels of omega-9s. However, the American diet has become heavy in omega-9s (largely from animal and processed sources), overly high in omega-6s (found in many plant-based oils, as for fried foods), and dangerously sparse in omega-3s (you know, seafood and such). Clinical studies suggest that altering our ratio of intake, rather than focusing on an individual fat type, is the most effective way to create positive biochemical changes in our bodies.

A review of recent research discloses mounting evidence that disturbances in fatty acid metabolism may link chronic psychological stress, endocrine responsiveness, and psychopathology. In particular, relatively lower omega-3 status corresponds to negative outcomes in physiological stress response. Research also suggests that the compositional changes made by our bodies to specific fatty acids may be able to serve as markers for stress and indicators for disease in the future (Laugero et al. 2011).

Click here and click here for fantastic sites to use while studying lipids!

Carb Overload

Posted: February 6, 2011 in biochemistry, chemistry

Ahhhh carbs. We all love them, we all love to hate them.

But what is it about a freshly boiled bagel, a pile of spaghetti, or a blueberry muffin that tempts us so? Well, that’s another discussion for another post. Namely, hormones. Which is two other posts, actually – lipids and polypeptides (protein).

For now, let’s try to understand the nature of the beast. What exactly is a carbohydrate? Are all carbs created equal? What’s the difference between “simple” and “complex” – and should I care?

Saccharides, generically called carbohydrates, are one of the four major categories of macromolecules – remember, this means that they have a carbon backbone with a characteristic functional group attached; additionally, they are polymerized into larger (more complex) molecules via dehydration (condensation) synthesis reactions and broken down in your cells using hydrolysis.

The monomers of carbohydrates, called monosaccharides, all have the same basic empirical formula: Cm(H2O)n. What this means is that the associated functional group is actually two hydrogens and an oxygen atom. For our purposes, remember this: The basic formula for a sugar is some multiple of (CH2O). For example, glucose has the chemical formula C6H12O6 – which is the basic sugar code times six. –Click here, click here!! JMol Glucose

Sugars and their polymers (polysaccharides) are the products of photosynthesis – these compounds are created to store the radiation energy from sunlight in tangible form. During that conversion process, energy becomes trapped in the chemical bonds holding together each atom in the sugar molecule. This potential energy can then be stored for later use, or be consumed by a secondary organism (such as us!).

Monosaccharides, or simple sugars, can be condensed together to form polysaccharide chains, becoming more complex(!) as they get longer and branch into bulkier forms. The more complex they become, the more potential energy they store in all those new chemical bonds. In plants, shorter saccharides, such as natural fructose, give sweetness and quick energy when we consume them, such as in fruit. Longer saccharide chains, such as starches, can take our bodies much longer to break down. Some sugar compounds are so complex that our bodies are incapable of breaking them down into the constituent sugar monomers (subunits); we generally call things in this class “fiber” – it passes pretty much right through us without being utilized for fuel. Even if we could process these compounds, our body makes the economical decision that it would cost more energy than we would gain.

Unlike plants, you and I do not store excess carbohydrates in our body. When we consume sugar polymers, we use them right away for short-term fuel supplies. A relatively small, finite amount more is stored as glycogen in liver and muscle tissue.

This is utilized in maintaining stable blood glucose levels and is available during the epinephrine (adrenaline) -induced “flight-or-fight”  response, and is what you are replenishing when you eat 30-90 minutes after a tough workout. Aside from building new muscle mass, however, there is no way to make your body store extra glycogen. Beyond this small reserve, any surplus sugars we consume are converted for storage into – you guessed it! – fatty acids. Lipids are our bodies’ preferred form of long-term potential energy storage molecules.

When you’re reading those ingredient lists, look for anything ending in “-ose” – this is the sugar suffix in chemical nomenclature, used to designate compounds your body utilizes as a short-term fuel supply.

The Stuff of Life

Posted: February 5, 2011 in chemistry

Recently a good friend turned to me and said something like this: My trainer tells me to eat all this protein and I don’t understand the carb thing and then where does fat come in, and calories, and sodium, and “artificial” stuff, and how do I know how to measure it all?

And I started to think about it…With all these chemical terms entering popular vocabulary, they are often misapplied and compounded and confused. What’s a grocery shopper to do about it all?

Answer: Learn chemistry. (Ha!)

Okay then – remember how we just learned what a calorie is? The amount of heat energy required to raise the temperature of one gram of water one degree Celsius. So a calorie is not a tangible “thing” but rather the energy given off during combustion of a substance. Which means we should examine the types of substances our body is capable of igniting! By the way, what is another word for “burning”? Oxidation, of course. And why is it that we breathe in oxygen for respiration? You guessed it!

There are three categories of macromolecules that we can manipulate and ultimately combust for energy. These (as I am sure you’ve read already) are lipids, polysaccharides, and polypeptides. You probably know these in general as fat, carbohydrate, and protein. Ah, but they’re so much more than these FDA-label terms!

Various molecules will burn with differing intensities, durations, and total (net) energy release. Consider the difference between lighting the wick of a candle and the wick on a stick of dynamite. The dynamite will obviously burn more intensely (violently), while the candle with a longer duration. What may not be as obvious is which gives off the most net energy. Over time, it is quite possible that your candle may release more total energy than the dynamite (or vice versa, depending on the specifications). In addition, the type of flame may be different – the nature of the fire itself changes with both the nature of the ignited substance and the conditions in which it burns. This comparison also applies to those substances your body combusts for fuel.

Of course, you already knew that – when you eat oatmeal rather than glazed doughnuts for breakfast, you have much more energy throughout the day; a handful of nuts is decidedly different than a handful of lettuce. “Artificial sweeteners” and Olestra and other diet (zero-calorie) substances are merely things that you can consume but your body is literally incapable of igniting. (Imagine trying to start a fire with sticks of glass.) But why? How does your body know what to do with what? And what does it matter?

To understand these questions one must appreciate the nature of macromolecules themselves. So let’s break them down and lay a solid foundation before we try to build upon it. I’ll independently address each of the FOUR categories of organic macromolecules in separate posts (visit this tutorial for an introduction), but provide a background below.

Since carbon can combine with up to four diverse partners, it becomes an essential backbone for organic molecules. Carbon skeletons form a structural basis, like scaffolding, for the building blocks of life – additions to this backbone are termed functional groups. There are six main functional groups in organic compounds; please study these in our notes. Almost everything that makes up our body is therefore built from the same basic components, just put together in diverse ways! Think of all the unique structures you can create with one simple set of LEGO blocks. Life reorganizes, because that makes more sense than reinvention.

Each of the four categories of macromolecules can be defined by the characteristic functional group(s) found attached to its carbon skeleton, and often also by a characteristic shape (spatial arrangement). The most simple component of each class is a structure that cannot be further reduced and still retain the properties of the category (much like an atom is the simplest structure retaining the properties of an element). This basic component is called a monomer (mono = single). Monomers of each class can be joined together into chains, called polymers (poly = many), during a process called polymerization. Alternately, these chains can be broken back down again (into the constituent monomer subunits) during a process called – you guessed it – monomerization.

Each type of macromolecule category is actually built up (polymerized) and broken down (monomerized) with the EXACT SAME process. Let me repeat: ALL TYPES OF COMPOUNDS IN OUR BODY ARE BUILT AND BROKEN DOWN USING THE SAME CHEMICAL REACTIONS. Once again, why reinvent the wheel?

The way all things, regardless of their type (fat, carb, protein, etc) are joined together into longer/bigger molecules (polymerization) is through condensation, or dehydration, reactions. These terms make sense, if you think about it – look up the standard definition of “condense” if you aren’t already familiar with it. When you are “dehydrated” it is because you’ve lost water. Likewise, when two monomers are condensed together, a water molecule is lost. Another way of saying this is that water is “given off” by the reaction.

The way all things, regardless of their type (fat, carb, protein, etc) are split apart into shorter/smaller molecules (monomerization) is through hydrolysis (hydro = water, lysis = to split … i.e. to use water to split!) reactions. This should now also make sense to you, if simply because adding water, or hydrating, is the opposite of removing water, or dehydrating (as in the opposite reaction, above). To break down large molecules, your body must add a water molecule between two monomers (subunits); this water molecule gets between them and literally splits them apart.

Chew on this: Why is it that you feel sluggish and don’t digest food well when you don’t have enough water in your system? Hmmm…..

Snow Days Inspire Innovation!

Posted: February 4, 2011 in chemistry, helpful hints
Tags: ,

Hey guys,

I’ll just assume you all have been missing me as much as I’ve been missing you! I hope you all are snuggled up with a good book (i.e. your biology textbook) and enjoying the surprise winter break. If you have running water, I’ll be there in an hour to borrow your shower…

I thought a biology blog might be a good way to keep us updated throughout the semester, and especially for now when we’ll be crunched to stay on schedule and cover all the required material. Please feel free to post information, provide feedback, and contribute in unique ways!

Hint: As you read through, make absolutely certain you understand every word/phrase used. If you don’t know the meaning of something used in context, LOOK IT UP. Don’t just continue past! To make for more condensed reading, I have chosen not to define concepts easily found in your book.

So from chemistry (continue reading through the notes, and I’ll also be posting more!) we’re scheduled to move on to cell structure and function. This includes cell theory, a description of various critical components, and a synthesis of how everything works together as a living organism. In multicellular creatures such as ourselves, our individual cells must then also be connected, both physically and functionally, to create a whole that seems itself irreducibly complex. For example, YOU don’t respire, your CELLS respire. You merely breathe; which allows oxygen to be disbursed to each individual cell, inside of each of which many semi-autonomous organelles called mitochondria actually perform the biochemical conversion of the glucose you eat into ATP fuel (think of it like an energy-storing battery) with the help of that oxygen.

Wow! Let’s back up a bit. While your body seems to work as a whole, it is composed of some trillions of individual cells – all derived from that single sperm-infused egg in your mama’s belly. Even though each (with one important exception) contains your entire genome, various “specialties” arise during your development and eventually lead to over 260 differentiated cell types that spontaneously organize into an integrated, functional system. In some (e.g. animal), but not all multicellular forms, cells may lose their individual identity to maintain that whole. Before we study the body systems, though, it is important to understand how each individual cellular unit works. In addition, it is important to keep in mind that most of life exists as single-celled organisms. And most of these are prokaryotic! For the purposes of this class, we’ll be focusing on eukaryotic cells like ours. However, I would like you to study, and be able to describe, the defining characteristics – and differences between – prokaryotes and eukaryotes in general.

Professor Wolfe (great lecturer) gives an overview of cells

Good cell overview with structure and function
Fun virtual tour (a bit technical in parts, but extremely informative) of the cell

I encourage you to play around on this website as you study
More great biology resources and videos can be found on Professor Wolfe’s website
Here are some tutorials with sample test questions from one of my favorite study sites

As we study the cell, you’ll notice that a major theme is the difference between the outside environment and the inner conditions required to maintain life. Homeostasis is the maintenance of the proper pH, temperature, osmotic pressure, etc. for optimal performance. The structure of the cell membrane itself is wonderfully crafted to very efficiently promote homeostasis. That is, it provides an effective barrier between external and internal environments – it is a selective, semi-permeable membrane. To fully appreciate this concept, one must be familiar with the chemical and physical concepts of diffusion and osmosis.

Osmosis and diffusion
Cell membrane basic structure and function
Excellent basic overview of cell membrane transport

Don’t forget that you already know all about diffusion and osmosis – why do salad bars and buffets keep veggies in water baths? To take advantage of osmosis (water in = fresh, plump appearance!)….but don’t be fooled! Where do you think the vitamins, antioxidants, and minerals are going due to diffusion? That’s right: If you want these nutrients, you’re probably better off drinking the water than eating the food (don’t really try that, by the way). And what about when you spend too long in the bathtub? You get all wrinkly because the same thing is happening to you! The bath water is hypotonic to your cells, which means that water diffuses (via osmosis!!) INTO your cells; you look wrinkly because they are becoming so individually overloaded that they are folding back upon one another as they swell.