Welcome back. This is the second video lecture for chapter 2, the chemistry of life. In this second video, we'll learn about organic chemistry. If you're looking to learn about or review inorganic chemistry, you should check out video one instead. Okay, organic chemistry. Let's reorient ourselves here. Recall that organic compounds always contain carbon and they're usually complex. Many are macroolelecules or polymers, meaning that they're made up of repeating subunits linked together. The major classes of organic compounds in biology are carbohydrates, lipids, or fats, proteins, and nucleic acids. One theme that you'll notice in the coming slides is that many of the example organic molecules we'll discuss are polymers. Polymers are macroolelecules, large molecules composed of many building blocks called monomers which are linked together. Polymers are made by dehydration synthesis reactions and polymers are broken down by the reverse hydraysis reactions. These reactions are catalyzed by enzymes. Don't worry, I'll describe these processes in much more detail as we move along and discuss each example of organic molecule. I just think that showing you this framework or pattern now will help you as you study. The first group of organic compounds we'll look at is carbohydrates, which are more commonly known as sugars and starches. Carbohydrates come in three main varieties. Monossaccharides are the building blocks, the basic single sugar units. Disaccharides are two monossaccharides linked together. And polysaccharides are long chains of monossaccharides. Let's go into each of these in a bit more detail. Monossaccharides are the simplest form of carbohydrates and are often referred to as simple sugars. The prefix mono means one. So monossaccharides are sugars composed of a single sugar unit and they can be used as building blocks for more complex sugars like disaccharides and polysaccharides. But monossaccharide units cannot be broken down any further into any smaller carbohydrates. Examples of monossaccharides include glucose, fructose, galactose, deoxyibbos and ribos. Monossaccharides are directly absorbed into the bloodstream during digestion. Whereas disaccharides and polysaccharides require breakdown using enzymes. This distinction really helps to highlight monossaccharides role as immediate energy sources versus storage or structural molecules. Glucose, for example, is the primary monossaccharide used by mitochondria in our body's cells to create ATP, adenosine triphosphate. And this is the energy currency that's used to perform cellular activities. So, how do you make macroolelecules like disaccharides and polysaccharides from monossaccharide subunits? They're built through a process called dehydration synthesis. When two monossaccharides, glucose units for example, are joined together to form a disaccharide like moltos, a molecule of water is released. This is why it's called dehydration, removing water. Similarly, when many glucose units link together to form a polysaccharide like glycogen, each bond formed releases a water molecule. This process allows cells to build complex carbohydrates by connecting simple sugar building blocks together while releasing water as a byproduct. So we use dehydration synthesis to make a macroolelecule. How do you break a macroolelecule? This process is called hydraysis which means to break with water. Take moltos again as an example. This is a disaccharide composed of two glucose units. In order to break that down, hydraysis requires that water be added. This water molecule helps to split the bond between the two glucose sugars, separating them back into their individual monossaccharides. Hydraysis is essentially the reverse of dehydration synthesis. It's how your body digests carbohydrates, breaking them down into smaller usable sugar units that we can use for energy. Once again, disaccharides, die meaning two, are two monossaccharides linked together by the process of dehydration synthesis. When we eat disaccharides, they get broken down during digestion using a process called hydrarolysis. Disaccharides need to be hydrayed into their individual monossaccharide subunits in order to be absorbed and used by the body. The hydraysis process is carried out by enzymes. Examples of disaccharides include moltos, sucrose, and lactose. Sometimes we have intolerances to specific types of sugars because we don't have enough enzymes to hydrayze the sugar for absorption. Take lactose intolerance as an example. Individuals with lactose intolerance don't make enough lactase enzyme on their own. So if they consume milk, ice cream or anything with lactose sugar in it, they don't have enough lactase enzyme to break down lactose into its component sugars for absorption. Instead, they need to take supplemental lactase pills like lactate to help to break down the lactose. Without lactase or supplemental lactade, these individuals can't break down lactose. But the bacteria in their intestines can and in this case the bacteria produce a lot of gas leading to intestinal discomfort. Polysaccharides are long chains of many monossaccharides joined together. The prefix poly means many. Polysaccharides are a great storage molecule. One polysaccharide that's very important for storage in the human body is glycogen. a long polymer of glucose. When there's more glucose than the body needs currently, it's stored as glycogen, a polysaccharide of many glucose units, which gets stored mostly in muscles and the liver. Athletes often practice what's called carbohydrate loading or carbo loading before endurance events by eating foods that contain a lot of carbohydrates like pasta and bagels. And they do this in order to maximize glycogen storage. Then during exercise when the muscle needs energy, it can break down glycogen into glucose in order to make ATP which can then be used for the muscles to contract. And this helps to delay fatigue and improve muscle performance during prolonged events like a marathon. Humans are only able to digest glycogen ingested from other animal tissue and starch glucose polymers from plants. Cellulose, another type of glucose polymer from plants, can't be digested by humans because of the particular type of bond linking the glucose units together. But it serves as an excellent source of fiber, helping to move feces through the colon. Hopefully by now I've convinced you that carbohydrates are a vital energy source for cells in our body. Complex sugars are broken down into glucose. Even other monossaccharides like fructose and galactose can be converted into the very important glucose subunit which is then used to produce ATP, the energy currency that powers cellular activities. And when we have a surplus of glucose after carbohydrate loading for example, we can store some of that extra energy for later in the form of glycogen. Beyond energy, carbohydrates also play an important structural role. For example, sugars form the sugar phosphate backbone of DNA and RNA, which is essential for storing and transmitting genetic information. Carbohydrates also decorate the surface of cells where they help to assist in cellto cell communication and immune system responses. The next type of organic compound we'll learn about is lipids. Lipids are a diverse class of organic molecules which are not soluble in water. There's a wide variety of structures and functions associated with lipids, ranging from serving as a vitamin all the way to cell signaling and membrane structure. But we'll focus on three main types of lipids. Triglycerides, phospholipids, and steroids. Triglycerides are fats and oils which circulate in the bloodstream and accumulate in fat tissue called atapost tissue. Structurally, a triglyceride consists of a glycerol backbone which is bound to three fatty acid chains. These bonds are formed through dehydration synthesis. The long hydrocarbon tails of the fatty acids are rich in stored chemical energy. When broken down, they release large amounts of ATP, which makes triglycerides an excellent long-term energy reserve. Triglycerides are stored mainly in atapost tissue beneath the skin and around certain organs. In addition to energy storage, these fat deposits help protect, insulate, and cushion underlying organs. So they contribute to both structural support and they also provide temperature and thermal regulation. Because triglycerides also circulate in the bloodstream and increase the risk of heart disease, it's important to consider different types of triglycerides. Triglycerides come in two main varieties, saturated and unsaturated. It's the length of the fatty acid chains and the prevalence of double covealent bonds that determines whether the triglycerides are either saturated or unsaturated. When only single coalent bonds are present between carbon atoms of the hydrocarbon tail, the adjacent fatty acid chains are nice and straight. So many fatty acids can stack together tightly and efficiently. So at room temperature, saturated fats can exist as a solid. Unsaturated fats are liquid at room temperature. When one or more double coalent bonds exist between carbon atoms in the hydrocarbon tail, the fatty acid chains get these kinks. And with these kinks, the fatty acids can't be packed closely enough together in order to solidify at room temperature. But instead they exist as oils. Mono unsaturated and polyunsaturated fats can be distinguished by the presence of one or many double coalent bonds. Foods which are high in saturated fats like red meat have been linked to an increased risk of heart disease by increasing blood cholesterol, contributing to plaque formation and narrowing blood vessels. and we'll learn about that more input oils are more hearthealthy. I should say these claims are very often debated and like anything there's nuance to the situation, but this is a good basic understanding. Saturated fats are bad, unsaturated fats are good. In case you're wondering or have heard about cis or trans fats, cis and trans has to do with the shape the molecule takes surrounding the double bond. Most saturated fats in nature have a cy shape which gives it that kink and makes it a healthier fat. Hydrogenated processed foods tend to have the trans shape and can more densely pack and form solids. Phospholipids are the second major type of lipid. They're sometimes referred to as modified triglycerides because if you look at their structure, they actually look like diglycerides with a phosphate group. They're composed of a glycerol backbone with two fatty acids and a phosphate group added. Phosphoipids are also said to be amphipathic molecules because they contain both a polar group and a non-polar group. The phosphate head of the phosphoipid is polar just like water. And because of this, it's considered to be hydrophilic or water loving. The fatty acid tail is non-polar and what's called hydrophobic, meaning that it it fears water or it's waterfearing. Phospholipids are extremely important because they're the main component of the plasma membrane in cells. They form what's called a phospholipid billayer, helping to separate the outside of the cell from the inside of the cell. The hydrophilic water loving phosphate heads face the watery environment outside the cell and the watery environment inside the cell. And the hydrophobic fatty acid tails orient themselves inward because they're non-polar. They don't mix with water. So they orient away from the water. Note also that the lipid portion of the phosphoipid is unsaturated. It has a double covealent bond kinking that hydrocarbon or fatty acid tail. This ends up adding to the membrane fluidity. The phospholipid billayer is kind of like an oil. the the plasma membrane is not solid. We'll learn more about this and its importance in chapter 3. Steroids are another important class of lipids in the body. They are organic compounds with a characteristic set of four interlocking rings of carbon. Examples of steroids include cholesterol, estrogen, testosterone, bile salts, and vitamin D. Cholesterol tends to get a bad reputation for its link to cardiovascular disease because high cholesterol can circulate in your bloodstream, clog arteries, and so on. But your body does need cholesterol. You use it, as it turns out, in your plasma membrane to help stabilize the plasma membrane so that it's not too liquid and flexible from all of those phospholipids in that phospholipid billayer. Cholesterol is also used as a building block to make all other steroids in the body like estrogen and testosterone, the principal sex hormones in females and males. Just to scratch the surface of what these hormones can do, estrogen helps to regulate menstrual cycles and pregnancy. Testosterone is important for the development of sperm, but also it's important for muscle metabolism. Cholesterol is also included in bile salts which helps the body to digest and absorb lipids during the digestion process. Your body also uses cholesterol to make vitamin D which is important for calcium absorption and bone strength. So steroids and cholesterol in particular are really important in your body. And you'll learn much more about these steroids, cholesterol uh in anatomy and physiology too. Proteins are another extremely important class of organic molecules. Proteins allow cells to to function and to do work. They are essential for nearly every structure and function in the human body. Proteins are polymers of amino acids connected to each other by peptide bonds. Another way to think of this is that amino acids are the building blocks for proteins. When you join multiple amino acids together using dehydration synthesis, you can create proteins. Proteins can have just a few or thousands of amino acids. For all the cells in your body to grow and function properly, you'll use about 20 amino acids. Your body can make almost all of them on its own, but you rely on getting nine from the food that you eat. These are the so-called essential amino acids. In other words, it's essential that you get them from your diet. Each of the 20 amino acids has common components. They each have an amune group, an organic acid group, and a functional group. The functional group is sometimes referred to as an R group as an abbreviation. The R group for each amino acid is what makes it unique. In the images of the amino acids below, you see first a generalized amino acid. Every amino acid has an aman group, an organic acid group, and a functional group, an R group. That R groupoup is the part that's colored green. In the other amino acid examples, you can see that they too have the same basic structure. They each have aman groups and organic acid groups. But what makes them unique and different from each other are their functional groups, their R groupoups. Don't worry, you do not need to memorize all the amino acids and their chemical structures or functional groups. The purpose of me pointing this out is simply for you to understand the basic structure of amino acids. To make a protein, you need to form peptide bonds between amino acids using dehydration synthesis. So, we start with two amino acids. Note that these are generalized amino acids. The R group is designated as R. If it were a real amino acid, you could include the real functional group, maybe a hydrogen if it were glycine, for example. But let's keep it simple. Removing water from the starting materials from those two amino acids forms a peptide bond between the two amino acids. They are linked together in what is now known as a deptide. To break a protein or in this case a deptide, you perform hydraysis which uses water to break the peptide bond. hydrate the amino acids to separate the deptide into its component amino acids. Hydraying proteins becomes important during digestion. You can break down the proteins you consumed into their component amino acids so that you can then use those building blocks, those building block amino acids to make whatever proteins you want. So if you wanted to continue to build on that deptide from earlier, you can continue to use dehydration synthesis to add additional amino acids to the deptide. And now you have what's called a polyeptide where many amino acids are linked together. When a polyeptide or a polyeptide chain is eventually folded into its proper three-dimensional structure, it then becomes a functional protein. Structure and function. Structure and function. H. This is beginning to sound familiar. And that's because proteins are a great example of one of the main themes in anatomy and physiology, the principle of complimentarity. The structure of a protein is extremely important if you want a protein to function properly. So let's learn more about a protein's structure and function. There are four levels of protein structure. The first level of protein structure is referred to as primary structure. The primary structure refers to the sequence of amino acid building blocks which form the protein. The exact sequence of amino acids is unique to each protein. And it's our genetic code, our DNA that serves as the blueprint, the instructions in other words, for our cells to know which sequence the amino acids should be in for each particular protein. The second level of protein structure is known as secondary structure. Secondary structure is the result of hydrogen bonds which form between the amino acids and caroxile groups of nearby amino acids. These bonds help to stabilize the overall peptide structure. Common shapes which are formed from secondary structure are called alpha helical spirals and beta pleated sheets. And the pleated sheets are kind of like these kinky zigzag sheets almost like you're folding a piece of paper to create a fan. The tertiary or third level of protein structure brings a three-dimensional shape. This should make it easy to remember. The third level of protein structure is the three-dimensional shape. The three-dimensional shape of the proteins actually comes from the functional R groupoups of the amino acids chemically interacting with each other. Lastly is the fourth level of protein shape or protein structure. Not all proteins develop this coordinary structure which forms as the result of multiple peptide chains interacting. Globular proteins like hemoglobin are a good example of a protein which develops coordinary structure. Hemoglobin is a protein that's located inside red blood cells which transports oxygen around your body. It's made up of four polyeptide chains that interact together. So, why is protein structure so important? Why go through the trouble of learning the different levels of protein structure? Remember, a protein's shape and structure directly determine its function. Mistakes in protein structure can be very bad. Take hemoglobin for example. A change in its structure might not allow it to bind to oxygen and then we would have reduced oxygen being delivered to the tissues in our body. Now, you might be wondering what can cause a change in protein structure and function. I'm going to offer you a couple examples. The first example is of a mistake in the amino acid sequence. If the amino acid sequence changes, the primary structure changes, but so too does the rest of the levels of protein structure. If the sequence isn't the same, then maybe nearby amino acids don't interact in the same way anymore. So the secondary and tertiary structure also changes. And if the three-dimensional shape isn't the same anymore, maybe multiple peptides don't interact the same way anymore. Well, gez, now you might be asking, what causes a mistake in the amino acid sequence? The short answer is a mistake in the genetic code, a mutation. DNA remember is what we use to determine the amino acid sequence. So if there is a mutation in the DNA then that can but not always change which amino acids get used. And when an amino acid is substituted it can change the way the peptide interacts and folds just as we described. Mutations aren't always bad. Sometimes, as we'll see next chapter, they might not do anything at all. But in some cases, it can end up changing the protein so much that it's completely non-functional or at the very least poorly functioning. Take for example cickle cell anemia where a veene amino acid takes the place of a glutamate amino acid. One mistake out of 146 amino acids in the entire beta chain of hemoglobin is going to cause a very big problem. Veene and glutamate amino acids are completely different. They have completely different functional groups. This has the effect of changing the shape of the hemoglobin protein in the red blood cells under low oxygen conditions. And this decreases the ability of the red blood cells to carry oxygen. If cells and tissues don't get their oxygen, they can die. Another way that you can change protein structure and function is through extreme mechanical forces or changes in pH and temperature. These changes can cause a protein to denature. What I mean by the word denature is that the protein can unfold. It can lose its hydrogen bonding, its secondary structure, can lose its R groupoup interactions, its tertiary structure, and it become and it can become non-functioning. Most times denaturing a protein is considered to be permanent. The protein albumin in eggs, for example, when physically manipulated to make a custard or when cooked at high temperature to make an omelette, are permanently denatured. When they lose their structure, the proteins will lose their function. In this case, we're just eating the eggs, so not a big deal. But let's not expose our body to these extreme forces. Okay? Once again, the reason why we care so much about the structure of a protein is because of the functions that those proteins provide to us. Here are just a few examples. Collagen and keratin are proteins which help to provide structure and strength to our hair, nails, skin, and bones. The proteins actin and meiosin are important to contract our muscles. Hemoglobin transports oxygen in red blood cells. There are numerous proteins which serve as hormones to regulate body functions ranging from growth and metabolism to sexual development. Antibodies, a key component in our immune defenses, help us protect ourselves against infection. Antibodies are proteins. All of these proteins, for all of them, structure and function are important to keep us alive. If the structure isn't quite right, then the function of these proteins and our survival may be at risk. The last example deserves some special attention. Some proteins serve as enzymes. What are enzymes? Enzymes are called biological catalysts. This means that they enhance the rate of a biochemical reaction. In other words, they help the reactions go faster. Rather than wait around for the amino acids to bump into each other in just the right sequence, we use an enzyme called pepal transferase to bring the amino acids together to get the job done faster. You could read the textbook and happen across all the information you need to learn for the exam, or I can serve as an enzyme to help introduce you to the most important information. Enzymes are proteins which serve as catalysts, meaning that they help to increase the rate of a biochemical reaction like the making or breaking of polymers. Importantly, enzymes don't just act on anything. Specific enzymes act on specific substances called substrates. For example, lactase is an enzyme which specifically acts on lactose, a sugar. It performs hydraysis of lactose, breaking it apart into its individual monomers, glucose and galactose. Another example, DNA polymerase performs dehydration synthesis, helping to link nucleotide building blocks together to form strands of DNA. ATPA aces are enzymes which break down ATP. They perform hydraysis to break down the phosphate bonds of ATP to release energy. In these examples, the lactose, the nucleotides, and ATP are examples of substrates. Note that the names of the enzymes typically reflect the substrate they act on. And usually the enzymes also end in the suffix ACE. Lactase, DNA polymerase, and ATPAS. Lastly, remember that the enzymes don't get changed in the reaction. Only the substrates get changed. After breaking down lactose, for example, the enzyme lactase is ready to break down more and more lactose. It's the lactose that gets changed in the reaction. Nucleic acids are the last type of organic molecules we'll discuss in this chapter. Nucleic acids are chains of nucleotide building blocks forming DNA and RNA. A nucleotide is made of a nitrogen containing base along with the backbone structures a pentos sugar and a phosphate group. For DNA, the pentos sugar is deoxyibbos, which should make sense since DNA is short for deoxxyribboucleic acid. For RNA, the pentos sugar is ribos. RNA is short for ribos nucleic acid. There are five different types of nitrogenous bases divided into two categories. Purines and puritamines. Purines the larger structure with the shorter name include adanine and guanine. Pyitamines the smaller structure with the longer name includes cytosine, thymine and uricil. Uricil is used exclusively in RNA. It is not used by DNA. DNA nucleotides pair with each other in a complimentary way such that a purine always hydrogen bonds with a puritamine. In DNA, adanine always pairs with thymine. Cytosine always pairs with guanine. The nucleotides monomers polymerize to form long chains of DNA thanks to an enzyme I introduced you to earlier called DNA polymerase. linked together, the strings of paired nucleotides form a twisted ladder we know as a double helix. The rungs of the ladder are the nitrogen base pairs and the sides of the ladder are formed by the sugar phosphate backbone. Importantly, the sequence of the nucleotides in DNA is what determines the sequence of amino acids when building proteins. Next chapter, we'll learn how to read the gene sequence in order to make RNA and make proteins. Here's a nice summary of the differences between DNA and RNA, which you should study and remember. DNA is located in the cell nucleus. RNA is located in the cytoplasm. The reasons for this will become more clear in the next chapter. In short, DNA serves as the genetic template to make protein, but it's far too precious to use on a day-to-day basis. So, we make a copy of it in the form of RNA, which is used to carry out the genetic instructions to make proteins in the cytoplasm. DNA contains deoxyibbos sugar whereas RNA uses ribos. DNA uses adanine, guanine, cytosine, and thymine as nitrogen base pairs. RNA uses adanine, guanine, cytosine, and uricil instead of thymine. In case you're wondering, RNA uses uricil as an analog for thymine and pairs with adanine when we are transcribing or translating DNA or RNA, respectively. More on this later. Lastly, DNA is double stranded. It has two strands of nucleotide polymers that interact. RNA, in contrast, is single stranded. It only has one strand of nucleotides. ATP or adenosine triphosphate is a special type of nucleic acid which remains as a single nucleotide. It's not polymerized like the nucleotides in DNA or RNA. Glucose or even lipids can serve as cellular fuel. But remember that they are broken down to create ATP. So ATP is the real energy currency of the body. The secret to ATP is the potential energy stored in the phosphate groups which are very tightly super coiled. Breaking the bonds between phosphate groups is like releasing a spring. Boing. And with it comes the kinetic energy to do cellular work. What kind of work gets done inside of your cells, you might ask? Well, that's a topic for the next chapter, cells. This is the end of chapter 2.