Chapter 2: If This Is Biology, Why the Fuck Are We Learning Chemistry?

Atoms: They Make Up Everything (I Went There)

I get it, you came here for biology and now I’m all “SURPRISE! Chemicals mother fuckers!” but at the heart of it all, biology is chemistry. We don’t have giant explosions but life is an endless series of chemical reactions that just so happen to make something alive. Its bonkers to think about because every single thing in the universe is made of the exact same three things: protons, neutrons, and electrons. No shit. Whatever you’re sitting on is nothing but protons, neutrons, and electrons. Same with your clothes (I’m assuming you’re wearing clothes because if you’re not, you’re seriously messed up. Put some clothes on you weirdo). Same with the air you’re breathing and same with you. The only difference between your underwear and you is how those three tiny ass little things are arranged around each other. Put them together one way and you have your tighty whities, rearrange them, add some more of one and a couple of another, combine them with their friends and you get the ass that is covered by those Fruit of the Looms. 

Together, protons, (usually) neutrons, and electrons make up the basic unit of matter, the atom. At the center of the atom is the nucleus (this word will show up again later, but in a different sense) and this is where you find the protons and neutrons. Together, these two components give the atom pretty much all of its properties with an important exception we’ll get to in a short bit. If you ask a chemist, they’d say that protons and neutrons are a difference size but for biology, they’re close enough. Equal in size, equal in mass, pretty much equal in every aspect but charge. That’s because protons are positive and neutrons are, hopefully you guessed this, neutral. So protons give the nucleus a charge while the neutrons add to its size. Think of an M&M; at the center of the candy is whatever we use to define the type. If its a peanut at the center its a peanut M&M, if it has a pretzel core then it is a pretzel M&M. I like to use to peanut M&Ms as an example because not only are they the best M&M type, the PeaNut reminds me of Proton and Neutron. Protons determine the peanut, neutrons determine how big of a nut it has (there is a joke to be made here about big nuts...I’ll let you have that one). 

All that being said, there’s always two other ingredients to an M&M that we haven’t discussed -- the chocolate and the candy shell. This is a biology book so we won’t get into crazy detail about electron orbital shapes and all that crap but I will discuss the importance of the cloud and valence electrons. If you already know what those two things are either you’re a chemist trying to brush up on biology or you have absolutely no reason to be reading this book. Either way, good for you I guess. Surrounding the peanut is a relatively thick ring of chocolate, and this is analogous to where our third atomic particle, the electron, is found. In the atom, this thickened area where you can find the electrons are known as the electron cloud because the electrons are somewhere within that area. We won’t get into why the word somewhere is emphasized in that last sentence in this book but hey, that’s what “High School Chemistry for Bastards” is for, right? Anyway with the candy, the chocolate and the nut are close to the same size but in reality, the area where electrons are found make up the vast majority of the atom and since the universe is made of atoms, most of the universe is empty space. Mind=Blown. 

Last anatomy-of-an-atom (or should I say...an-ATOM-y...dad jokes for days this chapter) topic is what the hell the candy shell is for. Yes, the shell is candy. No, its not chocolate. Yes, I’m sure. Imagine lightly closing your hand around a bunch of M&Ms and waiting a minute or two before opening your hand and dumping them out. What do you expect to see on your hand? The reason your hand looks all rainbow is because the outer candy layer protected the chocolate within. Back to the atom analogy, the candy shell is the same as valence electrons, which is just a fancy science way of saying “the electrons on the outside.” The valence electrons are going to be big shit later, just sit tight... 

Periodic Table Time

When you look at the periodic table, You’ll always see at least two numbers for each element listed. The smaller number is known as the atomic number and as easily seen, it goes one, two, three, all the way to one hundred eighteen as you move across and then down the table. More on what the atomic number is in five sentences. The other number (the bigger one) is the atomic mass. It’s usually some number followed by some decimal points (something like 12.01 in the case of carbon) and what that number represents is the weighted average of the atomic masses of the isotopes of that element. Lots of science words but stay with me as we work backwards through that sentence. An element is the most fundamental type of atom. Each element has a distinct number of protons, and that number of neutrons is what the other number on the periodic table tells us. Going back to carbon (because its a dope element and super important, more on that shortly), it has an atomic number of six, which means EVERY SINGLE ATOM of carbon in the fucking UNIVERSE has six protons. Let me say that again but in a different way because its super fucking important -- if any atom in the entire known and unknown universe has six protons, it HAS to be carbon. I screwed these last two sentences up the first time I wrote this because I was doing it at eight in the morning on a Saturday and accidentally wrote twelve (which is carbon’s mass) but carbon can’t have twelve protons because if an atom had twelve protons, it would be magnesium. Back to the good ol’ peanut M&M analogy, every single peanut M&M has to have a peanut at its center because otherwise it wouldn’t be a peanut M&M.

Just like the candy, which can have a bigger or smaller nut (insert joke from two paragraphs ago), carbon can have a bigger or smaller nucleus. How does this happen? By changing the number of neutrons. When you compare two atoms and they have the same number of protons but a different number of neutrons, they are what’s known as isotopes. Carbon has a bunch of different isotopes but some of the more famous ones are carbon-12, carbon-11, and carbon-14. Writing their names like this, with the element’s name followed by a number, we can actually get a lot of information if we’re smart enough to understand what the hell is going on. The word carbon tells us six protons because carbon’s atomic number is six and atomic number = number of protons. The numbers eleven, twelve, and fourteen tell us the atomic mass of that isotope, which is something we actually discussed earlier when the idea of the atomic nucleus was introduced. If you already forgot what you read three paragraphs ago, the nucleus of an atom contains all the protons and neutrons, so the atomic mass is equal to the number of protons (in this case, six) plus the number of neutrons. Carbon-11 has six protons and five neutrons. Carbon-12 still has six protons but this version of carbon has six neutrons, giving a mass of twelve. Lastly for this example, carbon-14 has, you guessed it, six protons and eight neutrons.

Also for each element, you’d have to be super dumb to not notice that every element has an abbreviation. Some are (hopefully) super obvious like C for carbon, H for hydrogen, O for oxygen, etc, but others, like those for potassium and lead, are definitely not obvious. Potassium is K, from the latin word for alkali (kali) which came from an arabic word meaning “plant ashes” People back in the day would burn trees to create potash, which is a substance used both as fertilizer and in the making of cement, and that’s why we abbreviate potassium with a K. The abbreviation for lead, Pb, is from the Latin word plumbum which means, oddly enough, lead.

The last thing related to the periodic table I want to talk about is how the number of valence electrons change as you move sideways across the table. Each column is called a group and starting in group one, with hydrogen, you have one valence electron. Group two has two, then things get fucked up in the middle and that’s another something for Chemistry for Bastards to cover, then group three has three valence electrons etc all the way until you get to group eight. What makes this important is the fact that atoms with the same number of valence electrons will tend to react the same. What do I mean by react? Well…

Chemical Reactions: Bringing the Boom (or Not)

Those valence electrons, hanging out on the outskirts of the atom, those fuckers are the important ones. They maintain the perimeter and they’re going to be the first ones to encounter another atom when they meet one. So when we discuss chemical reactions, what we’re really discussing is the action of one atom’s valence electrons in regards to those of another. Sometimes those interactions can make things go boom, other times they go sizzle, and still other times they seem to do nothing at all. But no matter the type of reaction that is occuring, really the only thing that’s happening is the atoms are rearranging how they’re grouped together. We’re not creating or destroying matter, just mixing it up. Conservation of mass if you want to sound like a smart ass.

We could spend a lifetime talking about chemical reactions and chemical bonds but we’re not because again, Biology for Bastards. Now in order for these reactions to take place, we have to put some energy into it at first. This is known as the activation energy and the best way to think of it is as gambling, which, as bastards, we do. You go to the casino, get the free drinks, and sit down at a machine. You can’t start playing right away, first you have to put money into it. Same thing with reactions. Some reactions are cheap, those are our penny slots, while others take a shit ton of energy to get going and are equivalent to our high rollers. No matter the energy required, you have to get to that amount before the reaction takes place. You can’t have half the energy and get half the reaction, it doesn’t work that way. You can’t play the ten dollar slots if you have five dollars. Just won’t work. Now sometimes, we can get away with cheating and using a catalyst to lower the cost. A catalyst is nothing more than something that speeds up a reaction by lowering the activation energy. It’s like having five dollars in free slot play so now you can do that ten dollar slot machine with your five dollars plus the free play cash.

So we’ve discussed what reactions are and how they happen, so now we have to talk about the types of bonds formed when these reactions take place. I know, chemistry kind of sucks and this shit just goes on and on but you’ll see why we’re focused on this at the end of the chapter (when actual biology starts to happen…). Technically there are three types of bonds but we’re not going to worry about one of them because we’re not robots. So ignoring metallic bonds, we have ionic bonds and covalent bonds. Ionic bonds occur when electrons are fully given up by one atom and fully received by another. On the other hand, covalent bonds occur when the electrons are shared by the two atoms. It’s like child custody: ionic is when one parent fully gives up their parental rights to the other and covalent is joint custody.

Just like joint custody doesn’t have to be even, neither does the sharing of electrons in covalent bonds. Sometimes, one atom ends up with custody of the electrons more than the other and when this occurs, a polar covalent bond is formed. (The opposite of a polar bond is nonpolar...no shit).  They’re called polar because they have a positive end and a negative end, just like a magnet. The negative side is where the electrons tend to hang out more and as a result, the opposite side is a little more positive. Polar bonds are super fucking important in biology because a lot of the elements we deal with (like oxygen…) make polar bonds and as a result, perhaps the most important interactions in biology can occur. What are these nearly mythical interactions that are responsible for keeping your ass alive? Hydrogen bonds. So important they’re called bonds when they aren’t actually sharing or transferring electrons. They’ve been promoted to bond level without doing bond work. They’re hot shit. Hydrogen bonds occur when you get two polar molecules together and the slight negative of one wants to pair up with the slight positive of another. I like to think of them as velcro (hook and loop fasteners if we’re avoiding copyrighted names…) because individually, a hydrogen bond is weak as hell. But when you get a bunch of them together they magically become strong as fuck. Hydrogen bonds help keep proteins together, help your DNA not fall apart and kill you, keep the world from being a giant ball of ice, all sorts of stuff. Like I said, they’re a big fucking deal.

Writer’s Soap Box Moment

You ever just stare at a glass of something with ice in it and wonder why the ice floats? No? Do you realize that the solid of everything else on the planet sinks if you throw it in it’s liquid? Throw a rock into a volcano and it’ll sink. Same thing if you put solid metal into some molten metal, Terminator 2 style, its bye bye T-1000. Not so with water. Water floats on it’s liquid and the way it is able to do so has everything to do with hydrogen bonds. When water is a liquid, the various molecules are drifting past each other fairly quickly, they dont have time to stop and get friendly with their neighboring molecules. But as the temperature drops and they move a little more slowly, they start to notice what’s around them. So around four degrees celsius, a magic event occurs. This is where water is as dense as it will be and as the temperature continues to drop, the molecules begin aligning based on the slightly positive and slightly negative ends and they spread out. Its not dissimilar to being able to tolerate being closer to people when you’re walking through a hallway but you wouldn’t want to be that close to them forever. You’d eventually want to spread out and face your friends. That’s what water does when it freezes and that’s why it floats. Which is a good thing because if it sank, every winter water would freeze and sink, piling up until the entire planet was a giant ice ball. If that happened, we totally we be dead. So thanks hydrogen bonds.  

Tripping on Acids and Bases 

Speaking of water, if you actually studied chemistry, you’d know that water is sometimes known as the universal solvent. Which means a lot if you know what it says but you probably don’t. Fortunately for you, this book exists. To understand that magical phrase, we first have to dive into the world of solutions. Life is nothing but a bunch of juices sloshing around together in sweet little juice sacks interacting with other juice sacks. Within those juice sacks, you have shit dissolved in water. That’s a solution. You can have a solution with other liquids but in biology, it's pretty much all dissolved in water. Water is the stuff in which the shit dissolves so water is known as a solvent. The shit, that’s known as a solute. You get a solution when you dissolve the solute in the solvent. So water is nicknamed the universal solvent because it can dissolve a whole bunch of shit and should always be the first try when you’re trying to make a solution.

Lots of stuff can be a solute but there are two special types of solutions that can form and those are your acids and bases. For the sake of me not caring and this being biology, we’re going to keep this part as short as possible. Sometimes when you dissolve stuff into solution, the solute breaks apart into charged little particles called ions. If those ions are positively charged hydrogen ions, you get an acid. If they’re negatively charged hydroxide (an oxygen hooked to a hydrogen) ions, you get a base. Using some weird ass math, we can measure how many H+ ions there are in a solution and when we do we get pH. I really hope you’re with me so far because this shit is boring and I’m not repeating myself. So once this pH is determined, we can create a scale from zero to fourteen (weird ass scale, I know). All you have to remember is seven is in the middle (basic counting skills) and the alphabet goes A then B. Start at zero, that’s an acid. When you hit seven (the middle) you change to B (for base). And just like on any scale with two options, the further away from the middle you get, the stronger that option gets. So zero is a strong acid and fourteen is a strong base. Something with a pH of 7.4 (like humans) is slightly basic. That’s right, ya basic. And we’re not going to get into any more detail than that because for life, if you get too far away from 7.4 (and by too far I mean like...7 or 7.9), you die. So there’s that….