Because I love sharing fun science stuff, here’s some fun science stuff involving time lapse, super HD photography of various crystals forming in solution.
Beautiful Chemistry has a lot of videos like that, from crystal formation to metal displacement, and they’re all awesome!
Story Time, kiddies! Gather round and I shall tell you a tale of The Little Protein That Could (and Would, Whether you Liked It Or Not).
Once upon a time there was a little protein. It was brand new and only 200 amino acids long. Which I suppose isn’t so little, polypeptide chains can be between 50 and 2000 amino acids long, but it’s certainly small compared to a lot of things., like a tissue or an organ or a schnauzer. Anyway, this was a denatured little protein, just a randomly coiled string of amino acids with only a primary structure to call its own. No secondary or tertiary, let alone quartenary structure! But it dreamed of folding into a functional protein, of finding its native state. Its friends had started out the same way, unfolded and unfunctional, but they had folded and moved on in the world. The little protein could not expect help from them. It couldn’t just try all the conformations available; that would take too long (to the tune of many thousands of years). So the little protein had to find help.
There were scientists studying all the proteins, but they were too distracted by the unpredictable coils of the denatured little protein (they understand very little of such things). Also proteins aren’t sentient and can’t talk. So the little protein had to rely on its self. Looking deep within (its primary structure), the little protein realized it had all the information it needed to folded within its primary structure! Insofar as proteins realize things (which is to say that they don’t). The very amino acids composing it could interact with one another via hydrogen bonds, disulfide bonds and other electrostatic interactions to find its energetically favorable native state.
Once folded, the little protein felt (“felt”) such relief (“relief”); the native state was a lower energy state than when it was unfolded. Now after its long (“long”, a fraction of a second) journey, it could go out into the world and follow its destiny (biological function).
The End.
Moral of the story: Look inside yourself and let your amino acids guide you.
Source
Sholders, Aaron. “Thermodynamics.” Biochemistry. Colorado State University. Fort Collins, CO. Jan 2013. Lecture
Get used to seeing lots of biochemistry in the coming months because guess what class I am taking! Ten points if you said biochemistry, twenty consolation points if you said Intermediate Snare Craft. To start with, y’all need some of the basic facts on protein. And I don’t mean that it’s one of the basic food groups.
First thing’s first: proteins are made up of amino acids, which in turn are composed of codons. I can only define all these things in a very round way, so bear with me. Remember the base pairs of DNA? They connect to two helices and are abbreviated with A, T, C and G. Identical base pairs are found in RNA (With the exception of T being replaced by U), which is like the paternal twin of DNA; they look very similar but are in fact very distinct. RNA provides the instructions for translation, literally the translation of genetic instructions into (hopefully) functioning proteins. Three bases make up a codon, which, depending on the codon, indicate particular amino acids for the translation proteins to assemble into the protein. Because I don’t want to take an even bigger detour, think of RNA as beading instructions. The codons represent an amino acid bead that needs to added to a string until you have the whole bracelet, or whatever.
Now the analogy gets a little funky. Proteins are made up of a combination of twenty beads (nine of which we can’t manufacture and need to consume, hence the nine essential amino acids) which start out as a string (or a peptide chain), but do not stay that way. The strand of beads is only the primary structure. Depending on the composition of the protein, the strand may fold into an alpha helix or a beta pleated sheet. Those are examples of secondary structure. The protein can then fold further into a tertiary structure, and then bind with other, separate strand in an oligomer (protein made of multiple subunit proteins). This oligomer is its quartenary structure. Consider an elaborate beaded necklace, like…this one:
We have two main strands of beads, with differently shaped groups attached. Now, some necklaces may need fewer separate strands and some need more, just as with proteins. An entire functioning protein may be fibrous and composed of many strands (silk, keratin, collagen, etc) and then it really looks like a necklace. But then there are proteins that are more like the beaded lizards you made in grade school. Bits and bobs EVERYWHERE. Make one out of beaded wire and smoosh it and then you have a globular protein. They’re kind of a mess, but they’re a necessary mess. Think enzymes and hemoglobin.
Homework for tonight: make beaded lizards and/or protein.
Send pictures.
Sources
Jackson, Mark. 2009. “Biochemistry Chemical Concepts.” Quick Study Academic Outlines. BarCharts Inc.
Photo credit, Swift’s Jewelry: http://swiftsjewelry.com/swifts_panamshoot23/
Story time, everybody!
So, right now I’m on a field research team working on the prairies of Colorado. Also right now, the temperature out where the deer and antelope play is stuck in the nineties. Needless to say, I bring a lot of water to work. But since I do not want my water to warm up too quickly and start tasting like old bath water, I freeze it overnight. This is very nice, but I can’t drink completely frozen water. Solid ice is just about useless when you’re thirsty. It needs to melt. Luckily, water (and everything else) has free energy. Free energy (represented by G) is a component of the total energy of a system that can do work at constant pressure. The system is the object or react in question and by work I don’t mean that free energy has a desk job or something. In physics, work is the displacement of an object by a given force. Push a book across your table/desk/park bench with wifi and you can say that you are doing work on that book. This also means you are transferring energy to the book, causing it to move. It’s like witchcraft. Minus the hoods and black goats.
Such evil things.
ANYWAY, if free energy changes, the system/my water bottle is undergoing some kind of reaction. If the change in energy is negative, that is, energy is exiting the system, then we say that the reaction is exergonic. Such reactions are also called spontaneous because they produce product under a given set of conditions and without any work until a reaction reaches equilibrium. However, when the change in energy is positive, energy is entering the system and we say that the reaction is endergonic. It is also non-spontaneous because the reaction won’t proceed toward product production without work being done. So where is my water bottle in all this? It is sitting in the hot Ford Explorer, and given those conditions it doesn’t have to do any work in order to melt. The bum.
Exergonic and endergonic reactions do not necessarily involve things heating up or cooling down. Explosions are a great example of exergonic reactions and they involve (quite a lot of) heat, but protein synthesis is an excellent biological example of an endergonic reaction that does not involve a drastic temperature change.
Now if you’ll excuse me, I’m going to go set up another exergonic reaction in my glass.
Cheers!
Sources
Hoffman, Kurt. “Work and Power.” Physics. Whitman College. Walla Walla, WA. 2011. Lecture.
Sholders, Aaron. “Thermodynamics.” Biochemistry. Colorado State University. Fort Collins, CO. Jan 2013. Lecture.
EDIT: Got my endergonic/exergonics confused with regard to ice melting. Fixed now!
So…Yeah…
Ahem, well! Everyone needs a vacation now and then so whatever!
Just to ease all y’all back into regular updates, I’m going to start with something soothing and relaxing.
Anyway, it’s time you kids learned some of the facts about water. Yes, water. In Seattle, between the rain and the Puget Sound, water is a popular topic of conversation. However! Outside of watering animals and plants, the properties of water are still under-appreciated. Yet, I have read and/or heard like, five news articles/tweets/telegraphs/telepathic broadcasts around town warning the unwary that, despite the high temperatures (Lower 80s. Yes, I know it’s not that high. Shut up), the Sound is still freeze-your-ass-off cold. But does anyone know why? Because water has a huge heat capacity. Thanks to the hydrogen bonds involved in forming the water molecule, it takes a LOT of energy for water to vaporize. As a result, large bodies of water act as “heat sinks” that moderate local climate. So Seattle and other coastal cities will not get nearly as hot or as cold as other places that are not surrounded by water.
If you’ve had instant coffee, instant soup, alka seltzer, Kool-Aid, etc, you have an inkling of the solvent properties of water. Thanks to the uneven distribution of electrons between the hydrogen and oxygen that compose the molecule, water is a polar substance. I has strong intermolecular forces, but most polar solutes can overcome this. Nonpolar substances, however, can and will and won’t dissolve like good little molecules. The rebels.
Probably the most important quality of water is its transparency. Without this simple quality, algae and water plants and phytoplankton would wither and then where would the rest of us be? Up Shit Creek without a paddle, that’s where.
So you damn well better enjoy the view guys, it’s the reason you’re here.
Source
-. 2010. GRE Subject Test: Biology 5th Ed. Kaplan, New York.
No, not that kind of pot, the copper kind. Maybe stainless steel, whatever you boil your water in. Anyway, it doesn’t matter the material, according to new research from Whitman University’s chemistry department, you may still have trouble making your tea in the morning.
Graduate students in the physical chemistry lab have shown that water heated over a low flame does not boil under observation. The Dunnivant Lab, headed by Professor Herbert Dunnivant, has been studying the various physical (as in the atomical and subatomical properties) of water for the past five years. Previous publications involved the potential of water to become a superfluid. A superfluid is a liquid that, once cooled to near absolute zero, possesses no viscosity, these actually “escape” from unsealed vessels containing them due to their lack of intermolecular friction. More recently, the Dunnivant Lab turned their attentions to water in higher energy states. In particular, the effects of different factors such as altitude, relative humidity and ambient temperature on the ability of water to boil and the temperature at which it boils. All studies were conducted with repeat trials testing the effect strength of the different factors when the flame was strong, medium or low. Most notably, observation had a significant effect on boiling point when the flame was low. However, if the water was heated with a coiled heating element (like an electric stove), boiling point was unaffected. All fire releases a certain amount of energy as photons or light particles. If unobserved, these photons dissipate as heat. But when you look at a flame, your eyes absorb those photons and they do not dissipate. This will actually lower the heat of the flame, but this is usually negligible. However, weaker flames are greatly affected by the loss of photon energy. To the point that an observed flame is unable to heat water to it 212˚ F boiling point.
So even though it may seem more energy efficient to use a lower flame when boiling water for your morning cuppa, as long as you’re watching and waiting, it won’t be. You can even test this at home. As we speak I’m typing from the kitchen where I set a pot on about an hour and a half ago.
I’ve been keeping an eye on it since and it still has not boiled. A candy thermometer held over the flame reads 100˚ F.
EDIT: Dammit, I looked away.
Source
Dunnivant, Herbert, Tanaya Raso and Emma Neff-Mallon. 2013. “The Effects of External Factors on Rapid Vaporization of Water.” Journal of Physical Chemistry. 101: 62-102
Sophomore year of my undergrad career, organic chemistry was the bane of my existence. I promptly burned all nonessential notes in the dorm parking lot when I finished that class. However! I’m not done with it yet, because I have to take biochemistry as a pre-requisite to vet school. Organic reactions and protein structures are HIGHLY IMPORTANT for surgery, apparently. In ways that not even any of the veterinarians I’ve spoken to can fathom. Deep shit, man.
So! First thing’s first: a small intro to orgo (emphasis on the “org”, as in “ORG I HATE THIS STUFF”). The “organic” in organic chemistry does not, in fact, refer to how natural the chemistry is. I’m sure those chemists are full of preservatives and growth hormones. No, organic refers to the kind of compounds involved; they are all carbon-based. The carbon atoms bond covalently to form molecules, which means that the atoms “share” electrons in their outermost ring (also called valence electrons). This also means the covalent compounds can only act weakly upon other molecules, so melting and boiling points are relatively low. Furthermore, covalent compounds require other covalent compounds for solvents and are insoluble in water. Try dissolving olive oil in water and you’ll see what I mean.
Different elements, depending on the group they’re in, can form a certain number of bonds. Not social groups, these elements are numbered and not free men (any Prisoner fans out there?). Look at the periodic table above and count the columns from left to right, ignoring the columns of transitional metals. Now you have your group numbers, these are the same as the number of valence electrons the number of covalent bonds each element can form.
OK, that is all the orgo I can take for now. Since I will just amble on my merry way through the subject, I welcome any questions to guide my academic wanderings.
Source
Meislich, Herbert, Howard Nechamkin, Jacob Sharefinkin and George Hedemenos. 2010. Schaum’s Outlines: Organic Chemistry. McGraw Hill, New York.
Time now to wander astray of the bio path and into the realm of chemistry. Frightening, eh? Well it’s about to get more frightening because I’m going to tell you about radiation.
Radiation is the emission of energy, such as light or heat. Unstable nuclei (the juicy, proton-neutron center of the atom) radiate particles to become stable. This is radioactive decay and as a result the nucleus may transform or move into a lower energy state. Basically, the nucleus is chilling out, working on some things, maybe taking yoga. Not really. Nuclei only have three ways to chill/decay, that is, via alpha, beta and gamma radiation. Alpha radiation involves nuclei shedding the equivalent of a helium nucleus: two protons, two neutrons. Beta particles are simply electrons or positrons (positively charged particles). Finally there’s gamma radiation, which involves the emission of photons and the alteration of the nucleus’ energy state. Now, what does this mean for safety? Alpha particles may be halted by paper, while beta and gamma particles require a sheet of gold or thick lead (respectively). If you don’t protect yourself, you could get radiation poisoning or turn into the Hulk. And no one wants that. But! Anything emitting alpha radiation is extremely dangerous if ingested, while controlled amounts of beta particle-radiating substances are used in radiation therapy. No joke, I had a general chemistry homework question that went like this: you have an alpha particle-radiating substance and a beta particle-radiating substance in lab neighboring yours. Will you experience any radiation while sitting in the next room? What if you walked into the lab and ate the alpha particle emitter? I wrote in my textbook that you have more to worry about if you’re eating random crap in labs. Also “no” and “yes”, respectively.
So kids, do your homework, it’s HILARIOUS.
Source
–. 2012. “Radioactive Decay”. Elementary Physics. 6 Feb 2013 < http://physics.bu.edu/py106/notes/RadioactiveDecay.html>
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