AP bioounit 1 is the foundation for all of the great biology that you'll be learning this year. Unit one focuses on the chemistry and properties of water and hydrogen bonding, the elements of life, and the four biomolecule families that all living things are made of. Carbohydrates, lipids, proteins, and the nucleic acids, DNA, and RNA. To help you study for this unit one test or the AP bio exam, I've put together a checklist that you can download at apbiosuccess.com/checklist. Let's go. Water and hydrogen bonding. First thing to note is that water is a polar molecule. There's unequal electron sharing between oxygen and hydrogen. And so there's a partial negative region over here. There's partial positive regions over here. Note that hydrogen bonds are intermolecular bonds. They're between molecules, not within molecules like covealent bonds or ionic bonds or anything like that. So what's happening is that the oxygen is partially negative. The hydrogen is partially positive and the hydrogen bond is a weak bond that forms between those two areas. Hydrogen bonds are much weaker much much weaker than coalent bonds, ionic bonds, any of those intramolecular bonds. Using the diagram below as an example, describe how hydrogen bonds can form between molecules besides water. The key idea is that hydrogen bonds are everywhere. They're not just within water. They're essential in biology in general. So in this example, there are two hydrogen bonds. And here's one oxygen to hydrogen over here. Here's another one between nitrogen and hydrogen. This is between the nitrogenous base adinine and thymine. And these are the hydrogen bonds that hold together DNA. Hydrogen bonds again are essential. They're um key to the structure of DNA, RNA, proteins. You'll meet them again and again throughout your biology course, and they're important to know for the AP bio exam as well. So now let's look at some of the consequences. So describe cohesion, adhesion, and surface tension and explain how these key properties of water result from hydrogen bonding. Cohesion, that's hydrogen bonds between water molecules. So this is cohesion right here. And it's responsible for many of water's very peculiar properties. It's a very small molecule, but it has a very high heat of vaporization. Takes a lot of energy to get water to evaporate. a high specific heat. It can hold a lot of heat and it has high surface tension which we'll talk about below. Adhesion is water sticking to other stuff. So like for example here you see hydrogen bonds between water molecule and the um cellulose walls that make up the conductive tubes of plants which are also called xyllem. A phenomenal thing is called transpiration, which is uh how water gets pulled up to the top of trees. And that's all based on water's ability to cohhere to other water molecules and to adhere to the sides of the conductive tubes of plants as water evaporates from the top. And finally, surface tension. Here we see a paperclip that's resting on a net of water molecules. And of course, that's ridiculously out of scale. You can see how that's keeping this paper clip from sinking down. And here it's the force exerted by water molecules on the surface of a body of water creates a kind of web or net upon the surface. In terms of hydrogen ions, hydroxide ions and pH describe the difference between an acidic and a basic solution. First thing to note is that um acidic solutions are solutions that have more hydrogen ions that here's a hydrogen ion over here than hydroxide ion. That's represented by O here. So if you dissolve this in water, you wind up having lots of hydrogen ions and that pushes the pH down. All right? Um the pH is below seven. In bases, there are more hydroxide ions than hydrogen ions. So if you dissolve sodium hydroxide in water, you wind up with a lot more hydroxide ions and that pushes the pH in this direction. PH is above seven. And one thing that I want to emphasize is that you don't really need to know about pH for the AP exam directly. There won't be a question about it, but it might be part of an F FRQ or a multiple choice question. So it's an essential underlying concept. Elements of life, topic 1.2 of AP Biology. So what do you need to know about the elements of life? Carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur. Sometimes referred to as chops. Carbon is the central element in all of the molecules that make up living things. Hydrogen often used in energy exchange. Uh we have molecules like NAD and NADH would show up in cellular respiration. NAD+ is the low energy form. NADH is the high energy form. You see stuff like that over and over again. And also hydrogen as an ion, as a hydrogen ion, a proton is often pumped around to create energy gradients. It's very important in the synthesis of ATP. It's the basis of acidity and alkalinity which we just talked about. But the main thing is to know about these atoms in context. Phosphorus is in phosphate groups which is found in ATP. That's the kind of interconnected crosstopic knowledge that you want to have for success in AP bio. Now we're on to topic 1.3 monomers and polymers and functional groups. So what are monomers? What are polymers? The basic idea is that three of the four groups of biomolecules, carbohydrates, proteins, nucleic acids are built from smaller building blocks that are called monomers. So here's a glucose monomer over here. Uh living things build macroolelecules. the big molecules, proteins, nucleic acids, polysaccharides, and that have specific three-dimensional shapes and shaped determines function um by combining these monomers into polymers. And a great analogy, if you hadn't already thought of that, is that the monomers are like Legos. You can combine them in any way to create other structures. And these big structures, the Millennium Falcon that you might have built as a kid or something like that, those are the polymers. And um here's a note about structural formulas. So if you see something like this, you might wonder like what's going on at these angles. Every unspecified angle vertex has a carbon atom. And um that that's why this is C6H1206 because there's carbons here, here, here, here, here. Carbon is so central that it's just understood. How do you put monomers together to make polymers? It's a process that's called dehydration synthesis. Everything in biology is run by enzymes as we'll see in unit three. And what enzymes do is they pull a hydroxal group over here off one monomer and it pulls a hydrogen off the other one. So here's the hydroxil, here's the hydrogen. That water is pulled out, right? Because this is H2O, the water gets removed and that creates a bond that's right over here. So here we see that between two amino acids and same thing. So two monomers becoming a larger molecule. Dehydration synthesis. Easy to remember. Synthesis is how you build things. And dehydration. When you're dehydrated, you lack water. So dehydration synthesis is pulling out a water. Now what about hydrarolysis? Hydraysis is the opposite of dehydration synthesis. Um in biology the suffix lice is very important and it involves breaking. So what happens in hydraysis is that an enzyme which isn't shown inserts a water molecule in between the two monomers making up the polymer. And what that does is it breaks them apart. Here we have lactose which is a disaccharide. I'll review that in a minute. It's a sugar that's made of two simple sugars that are bonded together. You add a water molecule and you get galactose and glucose. What do you need to know about functional groups? In one sense, not a lot. They're not going to directly appear on the AP bio exam, but in another sense, they're very important in terms of you decoding what's happening with the molecules in biology, which means the molecules that might appear on the AP bio exam or in your course. So, let's go through a couple phosphate groups. Number one over here, they're key for energy exchange. ATP, adenosine triphosphate. Phosphates are also found in DNA and they're what energize DNA monomers as they're put together. This methyl group over here at number two, it's used to silence DNA. It makes molecules nonpolar or hydrophobic. There are a couple of polar functional groups to know about. There's the hydroxal group at five, the carbonal group at seven, and they make molecules hydrophilic or water soluble. the caroxile group that's at number three and the amino group that's at number four. Those are essential in amino acids which obviously have an amino group over here have a caroxile group. Um the self hydro group over here at number six is very important in terms of protein structure. It uh creates a stabilizing bond that holds proteins in a specific three-dimensional shape. And the acetal group at 8 is used to activate DNA through a process called acetylation. So it's kind of the opposite in terms of function from the methyl group that we talked about carbohydrates and lipids. So what are the four types of macroolecules that make up living organisms? What can you identify from this diagram? So what you have here are carbohydrates represented by this disaccharide. Over here we have a lipid represented by a phospholipid, a key molecule membranes. We have a protein represented by hemoglobin and a nucleic acid represented by DNA. So those are the big four. What do you need to know about carbohydrates? Carbohydrates the monomer monosaccharides those are simple sugars and some of those are all important in biology like for example glucose which is essentially the fuel of life. Disaccharides are going to show up less in the course, but you might have a question that's about lactose and lactose intolerance. Well, really doesn't make sense unless you know that lactose is a disaccharide composed of two linked monossaccharides. And then you have polysaccharides, molecules that are used for energy storage like starch which is in plants, glycogen which is in you and other animals and then polysaccharides that play important structural roles like cellulose which makes up the cell walls of plants. While humans and other animals can't digest cellulose for food energy, a few animals such as ruminants and termites can explain. Most animals can't hydrayze the bonds that connect glucose monomers and cellulose. So here's cellulose. It's a polysaccharide. It's a bunch of linked glucoses, but it's linked in a way so that you don't have the enzymes that can break this bond, freeing up the glucose monomers. So essentially, you could eat lettuce, celery, these are high cellulose foods all day. You'd never get enough calories to really power your life processes. You do have the enzymes that can break this bond in starch. So over here and over here and over here and that enables you to convert starch into glucose and that enables you to use that glucose to power cellular respiration. There are a couple of animals such as termites and ruminants. Ruminants include uh cows, sheep, goats, deer, other animals, other mammals. And what they did is they involved symbiotic relationships with microorganisms that can hydraulyze this bond and thereby break this o excuse me break this bond over here break this bond over here break this bond over here and that releases these glucose monomers making food energy available. Let's end our review of carbohydrates by looking at an issue in relatively recent human evolution related to carbohydrates. And that's about the biology of lactose tolerance and intolerance. So here's what you need to know. Lactose is the sugar in milk. Here it is. It's a disaccharide. Lactase is the enzyme that hydrayes lactose into monossaccharides. And here you see that reaction happening. Most mammals only produce lactase during infancy while they're suckling because that's the only time that most mammals ever drink milk. So that makes sense from an evolutionary point of view because uh when you're an adult, you uh don't produce lactase. Why should you produce an enzyme for something that you don't eat? But what happened in human evolution is that some human groups that were pastoralist herders, these are people who um were associated with cows and sheep and goats and so on and so forth, they had access to all these milk products from the cows and the sheeps and the goats. And some of them developed a mutation that enabled them to continue to produce the lactase enzyme into adulthood. And that opened up a whole niche of food exploitation that wasn't otherwise available. Now, this didn't happen all over the world. This happened in a couple of hotspots. Here's one in Africa. Here's one in Europe. And here's one in uh Saudi Arabia, current Saudi Arabia. And here's one that is in the Indian subcontinent. And in those areas, lactase persistence, production of lactase into adulthood became widespread. But in large areas of the world that never happened. And there are many humans, the majority of humans who are lactose intolerant as adults. But if that's true of you, as it is of me, then we have products like lactade. Lactade is essentially lactase, the enzyme that you can use as an additive to food, and it'll break lactose down into lactose and uh glucose. And you can buy lactade milk and so on and so forth. And that's how that problem, if it's even a problem, is solved. Now, let's move on to lipids. Let's talk about lipids and what are their functions. So, here we have four different lipids. And what makes a lipid a lipid? First of all, lipids are molecules that are wholly or partly nonpolar. So, uh for example, like you see all these hydrocarbons over here, those are all completely non-polar. They don't dissolve in water. They're hydrophobic. They also are characterized by the fact that unlike the carbohydrates that we've met and the proteins and the nucleic acids that we will meet, they're not composed of repeating monomers. They might have subunits, but they don't have those subunits repeated hundreds or dozens of times. So, what are their functions? Well, over here we have um a fat, a triglyceride, and that's used for energy storage. That's true in both animals and plants. In animals, those fats are usually solid. In plants, those fats are usually liquid. We call them oils. Here's a wax. Waxes are used for waterproofing. This molecule is a phospholipid. It makes up cell membranes. We'll talk about that later. And then we have a steroid hormone like estrogen or testosterone that's used for signaling. So, what's the relationship between phospholipid structure and membrane structure? Well, here's what you need to know. Phospholipids have a hydrophobic nonpolar tail. That's this over here. And they have a hydrophilic or polar head. And those two parts are connected by a molecule of glycerol. And the key thing is that when you mix this kind of molecule in water, they spontaneously form an orientation where the heads will interact with water and the tails will avoid water. Hydrophilic over here, hydrophobic over here. And so if you can think about that arranged in a kind of spherical way, you wind up having a structure that is a bilayer, two layers of phospholipids. And that's the structural framework of cell membranes. We'll talk much more about that when we do unit two. At learn-biology.com, we understand why students struggle with AP bile. It's a hard course. The material is complex. The amount of vocabulary is ridiculous and the pace is withering. It's natural to feel overwhelmed and inadequate. To get an A or a four or five, you need an easier way to study. And that's why we created learn-biology.com. It's got quizzes. It's got flashcards. It's got interactive tutorials about every topic in the AP biocurriculum. It's got a comprehensive AP bioexam review system. Use learn-biology.com and you'll gain the skills and confidence to ace your course and to crush it on the AP bio exam. Here's your plan. Go to learn-biology.com. We've got free trials from June through March for both teachers and students. Sign up. You won't believe how much you'll learn. Let's review proteins. So, the monomer is an amino acid and it has a central carbon over here and connected to that carbon is an amine group over here that makes this basic in its structure. But over here on the other side, it's got a caroxile group and that makes it acidic or so. So therefore, it's an amino acid. There's a hydrogen atom attached to the central carbon. And then there's a variable group or an R groupoup. And there are 20 variations. And that's true of all life. All life is built of the same 20 amino acids. That R groupoup is also called a side chain. And it can be polar, non-polar, acidic, or basic. There are four levels of protein structure. This is a super important topic. We're going to do an overview and then we're going to walk through all four of these levels. Primary structure is what's shown over here in A. It's a linear sequence of amino acids. It's genetically determined. The secondary structure, which is shown here and here, those are interactions that involve what's called the polyeptide backbone. and you um do a dehydration synthesis and connect one amino acid to the next to the next to the next that chain of carbon carbon nitrogen carbon carbon nitrogen that's the polyeptide backbone. The next level is called tertiary structure and those are interactions between those R groupoups and then finally there's quturnary fourth level structure and that involves interactions between multiple folded tertiary peptides. Okay, let's talk about primary structure in this diagram. A1, A2, A3, those all represent different amino acids. So the sequence of amino acids that make up a polyeptide. That's what you call multiple amino acids linked together. That's the primary structure. Proteins aren't really built by enzymes in the way that everything else is. They're built by ribosomes. The amino acid, here's one, here's another one. They're connected to one another by peptide bonds. So I was saying before nitrogen carbon carbon nitrogen carbon carbon that's the polyeptide backbone. All of those amino acids that link together that's primary structure. What's secondary structure? Well, here you have a nice diagram that shows you what that polyeptide backbone is. And the secondary structure emerges as interactions between the carbonal groups over here and the um amino or amine groups over here within the polyeptide backbone. Now what happens is that interactions between these amine groups and these carbonal groups they form hydrogen bonds and they stabilize certain shapes. One of the shapes to know about is called an alpha helix and that's kind of a corkcrew over here. So you can see that there's a hydrogen bond that's stabilizing this hydrogen bond hydrogen bond. So that forms that shape. Now the other thing that happens is if the parts of the polyeptide chain are either parallel to one another like this or antiparallel to one another like this then carbonyl and amino groups can again interact and form hydrogen bonds and that can lead to a form called a pleated sheet and that's what we see over here. Tertiary protein involves interactions between the side chains or the R groupoups. And there are a couple to know about. First of all, there are hydrogen bonds shown at number two. There are ionic bonds that are shown at number five over here. There are covealent bonds which are shown at number three. That was uh between two sulhydral groups, another one of the functional groups. And this is a covealent bond that's very important in really tightly holding that protein into a specific shape. And then finally, you have what's called hydrophobic clustering where nonpolar side chains will cluster together avoiding water. Down here you see myoglobin which is an oxygen storing protein that's found within muscle tissue. That's a tertiary protein folded into a specific shape. And you can see like over here there's a whole bunch of alpha helyses that are in that structure. Hernomy structure involves multiple polyeptides that interact with one another to create the final form of the protein. So those interactions might be hydrogen bonds, they might be ionic bonds, they might be hydrophobic interactions. In this diagram actually you can see all four of the levels. So here's the primary structure. Here's an alpha helix secondary structure. This hairpin turn is actually um part of the tertiary structure over here. And then you have multiple polyeptides interacting. This molecule looks a lot like um hemoglobin. This is kind of cool in light of our recent history. The spike protein that's on the outside of SARS KV2 and in fact all the SARS viruses is also a quatary protein that's made of multiple folded polyeptide chains. An application of what we learned about proteins is this question. Describe the structure and function of hemoglobin and explain the molecular cause of sickle cell disease. So sickle cell disease is an inherited blood disorder. It was one of the first molecular um genetic diseases that was really well understood. The molecule that is in question here is hemoglobin. and hemoglobin its function is to transport oxygen in our red blood cells. The structure it's a quatronomy protein. It's made of four polyeptide chain. Sickle cell disease is caused by a recessive mutation. We'll cover that in unit five. But the key idea is that there's a mutation that causes the amino acid veene over here to substitute for glutamic acid. And that's an important mutation because glutamic acid is acidic whereas veene is nonpolar. The result of that is that when blood becomes deoxxygenated. Those mutated hemoglobin molecules they form hydrophobic bonds with one another. Well, why? Because they have a hydrophobic amino acid sticking on the outside and that causes them to do this. They cause uh fibers to develop within the cells and that causes the cells to become spiked like this. They're mutant cells and those cells will then clump up within smaller arteries and that causes these pain crises. It causes tissue damage. It's a debilitating disease. There are a few other things to know about cickle cell anemia. The first is that during the 30 years that I've been a biology educator, cickle cell disease has been transformed from a childhood disease with certain early mortality to a disease that can be managed with good medical care so that people can live into their 50s, 60s, and even beyond. Cickle cell disease is also a target for gene therapy, something that we'll talk about in unit six. And finally, there's a really interesting evolutionary thing where cickle cell disease evolved because having one copy of the gene is actually a benefit that gives you resistance to the tropical mosquito-born disease malaria. Something that we'll talk about in unit 7. And now for our last topic in this unit one review, nucleic acids, DNA and RNA. Note that we'll give an overview now and we come back to nucleic acids when we cover gene expression in unit six. So we'll start by describing the biological importance of the nucleic acids. These are the molecules of genetic information. DNA is the molecule of heredity. It's what passes from generation to generation. It's the molecule that cells pass on as they divide and replicate within a multisellular organism. RNA has other functions. RNA is the hereditary molecule in some viruses, never in cells. And RNA's key role is information transfer as in messenger RNA. So within a cell, here is DNA, the repository of genetic information. It has its information transcribed into RNA and then that RNA goes into the cytoplasm where a ribosome will translate that RNA message into protein. RNA is a very versatile molecule. It's not in the form of a double helix the way DNA is. It can take many many forms and it can act as an enzyme catalyzing reactions. Um, ribosomes are essentially catalytic RNA. There are also other molecules called splyosomes, microRNAs that play a whole variety of functions. And I finally want to say that this typically isn't put into this unit, but ATP is a nucleotide monomer. It's one of the monomers of RNA and it's the energy molecule of life. It's how cells get work done. What is the monomer of nucleotides? What's its structure? How are these monomers different in DNA and RNA? The monomers are called nucleotides. We just looked at ATP. All of these molecules have a fivecarbon sugar that's shown at number two. They have a phosphate group that's shown over here at number one. And then there's one of four nitrogenous bases. So the nitrogenous base doesn't have to have this structure. Note that the phosphate group is connected to a number five carbon whereas the nitrogenous base is connected to the number one carbon. When you learn about DNA replication, you'll talk about things like DNA is replicated in a 5 to3 orientation. And now you know that's about the five carbon over here and the three carbon over here. In DNA the sugar is deoxyibbos and there are four bases adinine thymine cytosine and guanine. In RNA the sugar is ribos and the bases are adinine uricil cytosine and guanine. Now let's talk about the structure of DNA. DNA consists of two nucleotide strands. So easier to see in this flattened out version. Here's one. Here's the other. Within each strand, the nucleotides are connected by sugar phosphate bonds. So here's a sugar, here's a phosphate, here's a sugar, here's a phosphate. But the strands connect to one another by hydrogen bonds. So here you see G connecting with C, A connecting with T. And those are rules to memorize. Adinine A always bonds with T, C bonds with G. They have complimentary shape. their molecular dimensions are such so that they fit nicely within the helix. That's more of a story for unit six. Um, and note that these two strands fit together in an anti-parallel orientation. In order for the nucleotides to form hydrogen bonds with one another, they each need to be upside down relative to the other. And that's what antiparallel is all about. We'll talk about this again more in unit six, but just to lay this down for right now, DNA is directional. Notice that in a chain of nucleotides, these are RNA nucleotides. You can tell because there's uricil. The nucleotide sugar binds with a phosphate. Then there's a sugar, there's a phosphate, there's a sugar, there's a phosphate. Well, the enzymes that build DNA, it's called DNA polymerase. And these enzymes, like all enzymes, have an active site. They only can work in certain orientations and they work by completely by feel and they can only add new nucleotides at the threep prime end of a growing nucleotide strand. So that's what directionality is all about. All of these nucleic acids are built in the fivep prime to threep prime direction. You can learn a lot more about unit one by doing our unit one review on learn-biology.com. Start with a free trial and you can learn a lot more about DNA by watching this song DNA fantastic.