Ch 2.5.5 - Proteins - No Clever Heading for These Molecules, They Deserve Your Respect

Proteins - No Clever Heading for These Molecules, They Deserve Your Respect

Ah proteins, the true workhorse of life. Basically if there is something to do, proteins do it. The only real exception is storing information because, as previously discussed, the douchebag nucleic acids do it and then need all the credit. Proteins are not only the real MVPs of life but they’re also some of the most complex members in the macromolecule lineup. Made up of thousands and thousands of individual units called amino acids, proteins can be as large or larger than nucleic acids. While there are only twenty unique amino acids, they can be linked together in any order they need to because three-fourths of the molecule is exactly the same for all twenty. There’s the amino (-NH) group, a hydrogen (-H), a carboxyl (-COOH) group, and then what is known as the R group. The R group is the only thing that changes from one amino acid to the next. When going through polymerization, the amino side of one will react with the carboxyl group of another, dehydration synthesis occurs resulting in the loss of water, and the two amino acids become linked with their R groups sticking off the side. Imagine taking a ladder and sawing it down the middle of all the rungs, the resulting structure would resemble a very simplified version of a string of amino acids.

This string of amino acids is known as a polypeptide because the bond that formed when we linked the two amino acids together is known as a peptide bond and now we have many of them. As we get larger and larger, we begin to start having interactions between various parts of the polypeptide and this is critical because as those interactions occur, the polypeptide changes shape and the way a protein functions is dependent on it’s form. You fuck up the form, you fuck up the function. All proteins have at least three levels of form, with the larger, more complex proteins having a fourth level. At the simplest level, known as the primary structure, we have the sequence of amino acids. This is the “half a ladder” structure I mentioned earlier. As the polypeptide grows, weak interactions (think hydrogen bonds) start to form between various places of the backbone of the molecule (so between the amino-carbon-carboxyl-repeat chain) and this presents us with the polypeptide’s secondary structure. Depending on the types of interactions and the frequency of them, the polypeptide chain can either coil into a spring-like alpha helix or do a sort of accordion fold into a beta sheet. As we get even more complex, we reach the tertiary structure where interactions between the side chains, also known as those R Groups, cause the polypeptide to fold, dip, duck, twist, doubleback, etc into what appears as a coiled mess but as we said earlier, is a very specific orientation. If the protein we’re focused on is a smaller, simpler protein, everything stops here. We have one polypeptide chain that has coiled, pleated, and folded into a given shape that can then go on to fulfill its duty. However, if it is a very large and complex protein, it may have a fourth level of organization known as the quaternary structure. This occurs when multiple polypeptides come together and is characterized by weak interactions between the various subunits.

Ch 2.5.4 Nucleic Acids - UGH, These Two...

Nucleic Acids - UGH, These Two...

While lipids may be the scapegoat and everyone hates them even though they’re super important and you wouldn’t even exist without them, nucleic acids are the Beyonce of the macromolecules. Sure they do something but they get so much credit for doing so little. Yes, they store genetic information. That’s it. GREATJOB NUCLEIC ACIDS FOR LITERALLY SITTING THERE! In their defense, that’s just DNA, the super overrated nucleic acid, that barely does anything. It stores information and then it...stores information. Once it’s done storing information, it stores information. Or gives you cancer. Yay DNA! Its cousin RNA is slightly more productive. It helps to read information and make something productive (proteins) out of the info. So it’s basically trying to salvage the image of nucleic acids by doing a little more than just sit there. 

Being nucleic acids (that’s what the NA stands for in DNA and RNA), they are both composed of monomers known as nucleotides. Each nucleotide itself is a polymer of three things: a phosphate group, a five-carbon sugar, and a nitrogenous base. The phosphate group is exactly the same for both DNA and RNA because a phosphate group can’t be different and still be a phosphate group. The sugar is almost exactly the same and is responsible for the first letter of the nucleic acid’s name. In RNA you have the sugar ribose and in DNA, you have deoxyribose. Deoxyribose is only different from ribose in the fact that in one specific location, you are missing an oxygen, hence being deoxyribose. Then there are five nitrogenous bases: adenine, guanine, cytosine, thymine, and uracil. The first three listed are found in both types of nucleic acids; thymine is found only in DNA while uracil exists only in RNA. In reality, thymine is just a slightly fancier form of uracil so that’s why they’re practically the same. 

Ch 2.5.3 Lipids - The Body’s Scapegoat

Lipids - The Body’s Scapegoat

Much like the carbohydrates we just talked about, most lipids are also composed of carbon, hydrogen, and oxygen but unlike carbs, lipids have a shit ton more hydrogen than they do oxygen. While they’re technically not true polymers, we talk about them at the same time as all the others because lipids are big, making them macromolecules, and they are important, making them worth your fucking time. Without lipids, we wouldn’t have any steroids, which include hormones, no fats, no waxes, and no cell membranes. We’ll come back to discuss the types of lipids found in cell membranes when we go through the parts of the cell so for now, we can discuss fats.

Fat has this negative image because a lot of people have too much of it and want to get rid of it but the healthiest of people still need some fat. When you look at professional bodybuilders, they’re still rocking a certain amount of body fat. Granted, it’s in the single digits percentage-wise but if they had zero percent body fat, they would be dead. (Coincidentally, a lot of them use extra lipids in the form of steroids but that’s not for me to judge.) Now when you look at a molecule of fat, you’ll see two distinct sections, the glycerol group and the fatty acid tails. Glycerol is an alcohol meaning it has at least one (it actually has three) hydroxyl (-OH) groups which serve as attachment points for the fatty acid tails by means of a dehydration reaction. The fatty acids are called this because at one end they have a carboxyl (-COOH) group. When the hydroxyl and carboxyl groups come together, a molecule of water is lost and BOOM! They’re joined together. Its entirely possible that all three fatty acids in a given fat molecule are exactly the same or they can be different, it doesn’t really matter.

What does matter is how those tails are constructed. The terms unsaturated fat, saturated fat, and trans fat come into play here and refer to the nature of the fatty acid. In an unsaturated fat (these are the “good” fats) there is at least one carbon-to-carbon double bond in at least one of the tails. In this sense, they are unsaturated with hydrogen. Alternatively, saturated fats are chocked full of hydrogens and everything is a single bond, single bonds as far as the eye can see. Comparing the the two, because of the orientation of the double bond in unsaturated fats (what’s known as a cis bond because the big parts are on the same side of the double bond), these fats can’t pack together as tightly as saturated fats can and as a result, unsaturated fats tend to be liquid at room temperature (all your oils) while saturated fats tend to be solid (butter, lard, etc). A trans fat is an unsaturated fat they turned into a saturated fat by a chemical process. They can also be partially-hydrogenated and in this case, the normally cis-oriented bonds become trans oriented, meaning the big parts are on opposites sides of the bond, and giving the trans fat its name. While this is no means a healthy living book, the majority of people say unsaturated fat good, saturated fat ok, trans fat bad.

Ch 2.5.2: Carbohydrates - why Keto is not Neato

Carbohydrates are delicious. No questions asked and no other answers accepted. I challenge you to find someone who doesn't think they're amazing and isn't a fucking liar because if they say carbs aren't angels in food form they're liars. Carbs get their name from the fact that they're made of carbon, hydrogen, and oxygen. When you combine hydrogen and oxygen, you get water and in science, we said the fancy word for water is hydro. So carbohyrdrate means carbon and water and any carbohydrate can be abbreviated by the formula (CH2O)n where n is a whole number. The most famous carbohydrate is glucose, which has a formula of C6H12O6 and is so fucking important it's stupid. Trust me, you will have that one memorized if you read this whole book. Glucose is definitely a monomer of the more complex carbohydrates (more on those in a few paragraphs) and being simpler in nature, glucose is known as a monosaccharide, essentially meaning one sugar. It’s what our bodies and the bodies of just about everything out there uses for energy on a daily basis. That’s why diabetes is so fucked up, it messes with your ability to essentially keep yourself energized. The sugar found in the infamous high fructose corn syrup is also a monosaccharide and when you hook fructose and glucose together (both being monosaccharides) you end up with the disaccharide sucrose, which is what you think of when you think of sugar. The white, crystally stuff found in pantries and that you put in coffee, that’s sucrose.

Once we start linking a shit ton of monosaccharides together, we end up with polysaccharides. Hopefully by now you’ve picked up on the fact that the word saccharide alludes to sugar but there’s another big name-based giveaway, something you’ll want to remember, that a compound is a sugar. So far we’ve discussed glucose, fructose, and sucrose, all three ending with the same three letters. That ending, -ose, is typically a dead giveaway that you’re talking about a sugar. (Side note: don’t be that fucker that says “nose” isn’t a sugar because that has ACTUALLY happened to me and it was so fucking annoying.) Polysaccharides can go by a bunch of different names because they can be countless different things but what we’re going to focus on are three major polysaccharides that are all formed by the same monomer -- glucose (told you it was fucking important). Starch, glycogen, and cellulose (there’s the -ose) are all polymers made of the exact same monomer, glucose, just arranged in different ways. Starch is made of thousands and thousands of glucose molecules strung together and serves as the main way plants store excess sugar. That’s why starchy foods like breads and grains are so full of energy and is the same reason low-carb diets work as long as you stick with them but fail the instant you start eating carbs again. Very similar to starch is glycogen, which is also made of thousands of glucose monomers except they are arranged in a slightly different manner than they are in starch. Glycogen is the animal form of starch and is basically the middle step between food that is eaten and fat being formed. Lastly is cellulose, which is also a bunch of glucose molecules stuck together in yet another different way and are arranged such that it is extremely difficult to separate the individual monomers from each other. Because of this, cellulose is less of an energy-storing carbohydrate and instead is a structural carbohydrate, being a major component of the cell wall of plants. 

Chapter 2.5.1 Kind of Chemistry, Kind of Biology, Let's Call it Chemology

Fine. It’s Actually Called Biochemistry

This gets to be chapter 2.5 because it’s still a shit ton of chemistry but it’s actually getting into biology (finally) and is important enough to deserve it’s own section. And I’m in charge and I wanted to do it. So while this field is technically called biochemistry, I’m going to stick with calling it chemology because it’s more fun to say and type than the alternative. So onward and upward with chemology!

In the last chapter, we discussed how life is nothing but a bunch of juice sacks interacting with other juice sacks and within that juice, we had solutes dissolved. Now, if we had to keep everything small and simple, life wouldn’t exist. It just wouldn’t. In order to do all the stuff we mentioned in chapter one that is necessary for life, we need some big ass molecules. HUGE molecules. How big are they? These molecules are so big they have to use a boomerang to put their belts on. (I can’t believe I just made a your momma joke about macromolecules...God help us all). They’re so big they get a special name: macromolecules. This literally translates to “large molecules” so bonus points on creativity there. Easiest way to make this stuff make sense is to imagine a paper clip chain or something similar. Maybe just a regular chain. Either way, something made up of a bunch of links. Or a trilogy of movies telling a single story. I could go on and on with analogies if I wanted to get my word count up but I’m trying to keep this concise so we’ll leave it with those two: a chain and a trilogy of films. The entire length of chain, or the full story arc is known as the polymer, meaning many -mers. Each link in the chain, or film in the series, is a monomer, which means, you guessed it, one -mer. Like the films, the monomers in a polymer can be unique things that fit together to create a larger unit (...larger unit...that’s funny) or, like in the chain, they can all be the exact damn thing. So all of these macromolecules we’re going to talk about are the polymer and each is made up of monomers, which themselves could be polymers made of monomers (with me?)

In biology, life is all about opposite but related actions. So if we're going to take the time and effort to create these large molecules, we're eventually going to want to break them apart. That's where the following reactions come in. Now before you get confused, try to keep up. Based on their names, you may be able to figure out that they both involve a water molecule in some way. Dehydration synthesis reactions are how you go from monomers, any monomers, and form a polymer. It's called dehydration not because you're losing a water molecule from the overall reaction (the real mindfuck is that you're actually producing one) but because you're pulling a water out of the reactants. One reactant loses a hydrogen and the other loses a hydroxyl group (remember, that's an oxygen and a hydrogen) and together that forms a water. The opposite process, where you introduce a water to break apart a polymer, with one part gaining a hydrogen and the other the hydroxyl is known as hydrolysis. Hydro meaning water and -lysis from the word to split, so it really makes sense that hydrolysis is splitting with water. This all makes more sense with a picture so hopefully when I actually publish this, it'll have a picture right…..here.

So let's talk about the different macromolecules and we'll start with the most delicious: carbohydrates

Podcast is UP!

It's been decided that a podcast needed to happen. Because everyone has a podcast now I wanted to be like everyone else. The plan for season one is to go through the AP Biology curriculum one chapter at a time until I reach the end. In the show notes for each episode will be a link to a matching powerpoint to really drive home the information

Be on the lookout for Biology for Bastards anywhere you get podcasts in the near future. Available now on Spotify, coming soon to Stitcher, Google Podcasts, Apple Podcasts,and all those other places where you get to listen to people talk to you. Hopefully this happens in the next day or two but with the weekend...who knows.

In the meantime, visit the website for the podcast here where you can listen to the first couple of episodes.

Ch 2.4: 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….