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.