BIOC 223

Lab on Monday made me realize just how important pH is for bio molecules. I had never before thought that slight changes in physiological pH could have such dramatic effects- even death? It felt to me that this dependence just made life unnecessarily difficult.

A few days back though, I saw something good about pH dependence. I was brushing my teeth and as I noted the alkalinity of my toothpaste, I realized what I was doing. I was increasing the pH in my mouth and making it really hard, almost impossible for bacteria to grow. I was glad that proteins are sensitive to pH and that our understanding of their biochemistry allows us to make use of this sensitivity and prevent tooth decay- among many other things

First read this really interesting article:
http://io9.com/physicist-proposes-a-thermodynamic-explanation-for-the-1507452119

If you’re really interested, here is the original published article:
http://www.englandlab.com/uploads/7/8/0/3/7803054/2013jcpsrep.pdf

By now, we all have come to intuitively understand why entropy is a matter of probability; for instance, our dorm rooms, no matter how organized we try to be throughout the week, will probably appear disordered by Friday.
Through spontaneous mechanisms, the universe tends toward maximum disorder, both in politics and BIOCHEMISTRY. I think it is wonderfully beautiful that while all life forms, us included, are highly intricate, ordered structures, our creation and continued existence, by using up energy, and by definition, being an open system, does in fact increase entropy.

The article above discusses Dr. England’s ( MIT) theory on how life originated, whereby he uses thermodynamics to explain the evolution of organisms, starting with plants in aqueous environments, being exposed to sunlight. The article also touches on many of the food related examples I think people find to be interesting, concerning why for instance a cooked egg does not resort back to its native structure in terms of proteins.

For Dr. England, the theory is very much intuitive and logical:
“Particles tend to dissipate more energy when they resonate with a driving force, or move in the direction it is pushing them, and they are more likely to move in that direction than any other at any given moment.”

Could the wonderful mystery of how a nano-scale prokaryote evolved into the complex beings we are be explained by what he describes as common sense theory concerning the natural dissipation of energy? It’s certainly interesting!

We have/had to sign up for our favorite biomolecules today and, quite honestly, I really don’t know much about anything except nucleic acids (from research/genetics) and proteins (from cell physiology). So I decided to put in a little research before I made my choices, and it got me thinking about food.

Food, when you really think about it, is very, very weird. I am distinctly aware of this fact every time I go to the dining halls and realize that I’d rather start being anorexic than eat there. There’s a quote from a TV show I once saw that I really liked. This is going to be terribly cited, because I can neither remember the TV show name (it ran for only one season and was about a teenaged girl who made a new friend and dyed her hair red) nor the actual quote, but it went something like this: “Have you ever thought about chewing? Like, what it really is? And people that do it all the time, in public!”¹ Like the rest of the season, this comment was funny because of how true it is. Chewing is weird. And, as it turns out, so are proteins, carbohydrates, lipids and nucleic acids.

The concept is simple, but before today, I had never really thought about exactly why we eat or what it does for our bodies. I had heard, of course, about ATP and energy storage, etc., etc., but I hadn’t really taken the time to consider the fact that as I put a piece of meat into my mouth I am tearing apart the tissue down to it amino acid composition and then reorganizing all of those amino acids into my own proteins.Literally. I am the chicken that I put in my mouth when I was 5. Or, at least, a part of me could be. (The same is true for our nucleic acids.)

In this vein, carbohydrates are a little more palatable (no pun intended). We eat the carbohydrates, we break them down into useable saccharides, and then we release the energy into NADH and ATP. (AP Biology is all coming back to me!) No weird chicken-is-me pseudo reality.

But lipids, which don’t even dissolve in water, are equally strange. Have you ever considered what it must be like for your body when you digest a saturated lipid that’s solid at room temperature? Where should it go? Not only will it not simply dissolve in, it won’t even liquify if you put it too close to the surface! Ugh. How odd.

In any case, I am very excited for all that we will discover about these biomolecules in the coming months. I hope to be appropriately disturbed each time I sit down for a meal. Bon appetit!

¹Fun aside: In trying to find my chewing quote, I came across a Wiki How on How to Chew Gum in Class (in 15 steps). Check it out: http://www.wikihow.com/Chew-Gum-in-Class.

Coincidentally, the article immediately below in my Google search was “Why Chewing Gum Destroys Your Health” (s ee http://foodbabe.com/2011/12/09/wanna-a-piece-of-gum/), which continues the conversation of food to the topic of the food industry, and my thought “is what we are putting in our mouths actually classifiable as food, or at least something we would like to eat?” Hopefully I’ll have more of this to come in future blog posts!

Freshly out of the shower, I walked across campus this morning with my hair still wet. In the sub-0°C air, my hair froze almost immediately. I entertained myself thinking about the hydrogen bonds I broke and allowed to re-freeze as I shaped my hair into funny designs, which stuck around as long as I was outside. Most of the time, I warmed my hair between my fingertips before shaping it so that I didn’t hear any sounds as bonds broke, but every now and then there would be a louder crack as the ice crystals snapped. I wondered, as I heard that cracking, if I was breaking a few covalent bonds as well as my good friends, the hydrogen bonds.

Since I was thinking about biochemistry, I had two other natural phenomena on my mind. The first had to do with my poor aloe plant. Unfortunately, my aloe plant now sadly droops inside my house, with visible air blisters. The other night, my friend and I forgot about it in her car and it froze. We suspect that the ice crystals tore apart the plant cell walls, since the sad thing is now unable to keep its leaves up.

The second phenomenon I thought of was diamond crystals. How funny – and unpleasant – it would be if our hair were frozen in diamonds instead of water. So I started thinking about the composition of hair, and decided to look it up. It’s predominantly made of keratin, with cysteine amino acids bonded together by disulfide bonds in a repeated, twisted structure. Though predominantly carbon, like the rest of us, it’s interesting how differently carbon structures are manifested depending on their repeating units (e.g., graphite in comparison to diamond’s crystal lattice). We have little concern that our hair carbon atoms will spontaneously form diamonds, because the Gibbs free energy is much too positive. But if our hair did freeze into diamonds, I would certainly not be able to shape and reshape it so easily!

I also found that hydrogen bonding also holds the hair protein chains in their long, repeated units. I wondered if, unlike diamond structures, these hydrogen bonds are what allow our hair to bend, and unlike my aloe plant, also to freeze and unfreeze without breaking apart. I couldn’t find any especially reliable source on the internet, but I would be interested in your thoughts!

Hi all,

I also thought it was great that food has been a central topic in many of these blogs! To continue with the trend, I decided to focus on one of my favorite dessersts: meringues.

I was out in Cambridge this week and as a little treat to myself, I stopped by Flour and ordered a small almond meringue. I normally have a set order when it comes to Flour, but most anything you can get there is equally delicious. The meringue was no exception!

One reason why I am so fond of this light, sweet, and air treat is its unique texture – a crunch, and a delight of weightlessness. (Economically, it’s a very smart product to sell. I spent $2.00 on a whole lot of nothing!)

Egg whites are the main “magical” ingredient in meringues – and it’s whipped into a frothy mixture. Perhaps we didn’t fully realize this but denaturation can occur by physical breakdown as well. (I also remember Prof. Oakes talking about being careful when pipetting our protein solutions, and how frothy solution meant we had damaged our proteins in some way.)

When you beat the egg whites, you are introducing air into the system of proteins, which causes the egg proteins to rearrange itself into a more favorable state. The hydrophilic parts of the egg protein immerse themselves in water, but hydrophobic parts are more attracted to air and thus stick out. This rearrangement then forms more bonds with each other in their current arrangement, which can trap the air bubbles in place, resulting in a bubbly, frothy, protein network.  More details are in the link posted below!

Whenever I saw my mother make meringues, I would see the frothiness rise forth, but I had never considered what was happening on a protein-scale level.  I feel as though from our discussions on this blog, we will never be able to look at anything with same mindset ever again…

Source: http://www.exploratorium.edu/cooking/icooks/11-03-03.html 

So in my blog today I’m not going to be covering necessarily a biochemistry concept in terms of covalent bonds or interactions or pKa’s or the like, but rather a process that we all got familiar with on Wednesday night and that we, as potential future biochemists, will probably encounter often in our respective fields. I am talking about the process of solving puzzles and the art of making inferences!

Solving puzzles is not unique to biochemistry, obviously. I will argue, however, that biochemical puzzles are one of the most satisfying scientific puzzles to solve, simply because we have an amino acid alphabet to work with, which is a little more tangible than say, quarks or antimatter and other things of which we don’t actually understand the physical makeup. At least for amino acids, we know what they are supposed to look like, chemically and physically!!

In the review session, we spent ample time on some of the problems trying to piece together the results of various protease assays to determine the peptide sequence. This reminded me so much of scavenger hunts I used to play as a kid or programmes I used to watch on TV (Wheel of Fortune, Hangman, etc) — except this was one better! Because we were not trying to guess and anticipate words, which is delicious in a different way, but rather we were using our biochemical knowledge of each protease’s tendencies and cutting signatures to construct a logical sequence.  I was also reminded of newspaper rooms before printing day, when the editors would cut out pieces and segments of stories to form, quite literally, a coherent story, a logical flow of ideas and articles.

As we were all enjoying the puzzles from the worksheet, I began to think a little quasi-profoundly, “Aha! So this is why I have always been drawn to science!” I really am not kidding about that, haha. Science is satisfying.  At its core there is a cause-and-effect relationship between every experiment you run. Although you might not understand everything in the realm of science, if you possess enough logic, you can make inferences, and use those inferences to make a logical construction of a guess. At the end of the day, it really is just a satisfying process, and to me nothing is more desirable than the feeling of satisfaction.

I unfortunately have to admit that I have never seen a diamond melt, and I’m not sure I’ll get a chance to witness such an event. However, with all the snow flurries today, we can all say that we have seen the phenomenon of ice and/or snow melting! In class today we learned that ice is not just bound by a network of H bonds, but a composite of covalent bonds (O-H in the actual water molecule) and H bonds (attraction of O of one molecule to H on another molecule).  The fact that H bonding is a component of its solid crystal formation explains why the melting point for ice is much, much lower, relative to diamonds.

Because of this, I was wondering how snow, which is a form of frozen water, differs from ice. I don’t think it would differ chemically, but surely something about the two frozen forms must be different, because they appear so different to us as observers, in terms of shape and size. Even snow can come in multiple ‘forms’ – it can be delicate, soft, fluffy, clustered, tiny….and anything in between. I was wondering how the chemical structures of these different forms of frozen water are different, if at all.

I looked up some articles online, and got a small sense of how snowflakes form!  Snow forms from water vapor in clouds, but can encounter many obstacles on its journey down from the sky. Because each snowflake embarks on a different journey, so to speak, it will form different crystal structures that we can delight in here on the ground. For example, if snowflakes form in colder temperatures, they will produce lacy, delicate hexagonal snowflake shapes. If snowflakes are formed in warmer temperatures, the snowflake forms more slowly, which unfortunately means less elegant structures. The presence of dust particles also can affect crystal durability. Furthermore, since weather can fluctuate, a water vapor can undergo snowflake formation, can partially melt, and reform multiple times before it hits the ground.

However, if I interpreted it correctly, all these beautiful structures still are the result of good old hydrogen bonding. These H bonds are often responsible for the symmetrical shape of snowflakes because that represents the most ordered internal structure of the freezing water vapor. The process of crystallization, with the help of H bonds, aligns water molecules in the most favorable way, resulting in the delightful structures we see.

My second question I’m posing, inspired by our discussion of melting in class today – Why is water wet? This question is a little more philosophical than biochemical, since I think wet is a description we assigned to the sensation of feeling liquid things, but I thought the responses to this question (in link below) were very satisfying because it again emphasizes how differently people can respond to a probing but ultimately simple question.

http://www.theguardian.com/notesandqueries/query/0,5753,-1725,00.html

I think one of the concepts we had this week that was most interesting to me was our discussion of water, often known as the “universal solvent” or the “solvent of life”. This is, in my opinion, a very true moniker; as organisms need water to survive. But perhaps on a less immediate scale in my everyday college student life, water is very necessary because I need it to make my weekend hot chocolate. I enjoy the convenience of the instant hot chocolate packs, though I’m usually too busy enjoying the drink to think about the chemistry/biochemistry behind it.

One packet of Swiss Miss Instant Hot Chocolate contains: sugar, corn syrup, modified whey, cocoa (processed with alkali), hydrogenated coconut oil, nonfat milk, calcium carbonate, less than 2% of: salt, dipotassium phosphate, mono- and diglyderides, artificial flavor.  This seems like an even mix of polar/easily dissolvable (sugar, calcium carbonate, dipotassium phosphate) and nonpolar  (coconut oil, nonfat milk, etc) substances. As such, I would think room temperature water would not be as effective in dissolving this mixture. However, once I add boiling water and give it a stir (to increase surface area/expose solute to solution), I have -voila!- drinkable hot chocolate.

I think it makes sense that temperature increase the solubility of a solute, in this case hot chocolate mix, because the system is given more energy required to break the bonds of the solid. My question is, if the solute is nonpolar, does temperature increase the nonpolar solute’s solubility? Does its nonpolar nature even matter? Observationally, I’d have to say no. I guess a bond is a bond and a bond is meant to be broken. (Though would love to know if this is true or not!)  At any rate, upon reflection of this process, I am glad that water is the universal solvent – it’s rather tasty by itself and when making hot cocoa.  I can’t imagine having to make my hot chocolate with some other sort of liquid!

There is so much overlap between my microbiology class and biochemistry! We recently read a paper about the changes made in gut microbiomes as diets change between vegetable-based and animal-based, including microbial genes coding for amino acid synthesis molecules that were up-regulated or down-regulated based on diet type. Vegetarians needed more support from their microbiomes to synthesize amino acids, and they acted in different pathways than meat-based diets. It got me thinking about the ways our bodies have to adapt in order to keep all 20 amino acids at the correct levels in our systems, which is so important to human health! If you’re interested in the paper, you can find a PDF here: http://obs.rc.fas.harvard.edu/turnbaugh/Papers/David_nature12820.pdf