introduction to organic compounds

Welcome to our introduction to Organic Compounds.

Organic molecules are molecules that consist primarily of carbons and hydrogen atoms. Carbon atoms bond covalently with up to four other atoms, and so they can form long chains or rings or various diverse structures. As a result of the versatility in bonding arrangements for carbon, organic molecules are also highly diverse, and so organic molecules are the molecules of life. Carbohydrates and proteins and lipids and nucleic acids. These are all organic molecules. They are all carbon based molecules. And a general rule of thumb to remember is that there can be up to four bonds to carbon. Once again, for bonds to carbon in organic molecules.

The learning outcomes for today include an introduction to organic compounds, a discussion of carbohydrates, a discussion of lipids, a discussion of proteins, and a discussion of nucleic acids.

The molecular diversity of life is based on the chemical and physical properties and the bonding characteristics of carbon. Almost all the molecules a cell produces are composed of carbon that is bonded either to other carbons or atoms of other elements, and so carbon based molecules called organic compounds form the basis of life. Here is a depiction of a simple organic compound, methane. I should point out some conventions here. The black sphere conventionally represents a atom of carbon, and the white spheres conventionally represent hydrogens, and the lines or sticks in the figure represent shared electrons or covalent bonds, and so the formula for methane is CH4, and it consists of a carbon covalently bonded to four hydrogen atoms. Notice that the structure is specific. The structure of methane is called a tetrahedron. Briefly it looks like a pyramidal 3D structure. The lines or sticks, as I mentioned in the diagram, represent shared electrons, and so by sharing electrons, carbon can bond to four other atoms or branch and up to one, two, three, four different directions. C-H for a methane is one of the simplest organic compounds as a result. There are four covalent bonds that link the four hydrogen atoms to the carbon atom, and each line or stick in the figure represents a pair of shared electrons. Now methane and other such compounds. Other organic compounds.

Composed only of carbon and hydrogen are called hydrocarbons. And carbon with attached hydrogens can form chains of various lengths and various conformations. A carbon skeleton is what we call a chain of carbon atoms that differ according to whether they are straight, whether they are branched, or whether they are arranged in rings, and in fact, they also differ in their lengths. And so let's look more closely at various carbon skeletons. Here is a carbon skeleton comprising two carbons. And this is called ethane. A three carbon organic compound shown here is called propane. Propane is familiar because it's used as a gas commercially in things like barbecues and so on. And so the length of the carbon skeleton can vary.

What can also vary is the number of bonds, that is, covalent bonds between carbons. Here is a four carbon organic molecule called one butane. The one refers to the location of what's called a double bond. This is an instance of two covalent bonds between two adjacent carbons. And so the location is revealed by the number. And this is called one butane. It has a double bond between the first and the second carbon. This is two butane where the double bond is between the second and the third carbon. Notice that these double bonds occur in organic compounds that are linear in arrangement. Here is butane. And butane lacks double bonds between carbons and also has four carbons in its structure. And here is iso butane. This is an example of what we call branching. By maintaining the rule of thumb for bonds to carbon, molecules can still arise or be synthesized that are diverse in shape. And so iso butane has a branched carbon skeleton. In fact, ring structures are also possible. This is cyclohexane. The hex in cyclohexane refers to the presence of 123456 carbons. Each carbon, as you can see, is engaged in four covalent bonds. Total. Maintaining the rule of thumb for bonds to carbon. And the carbons have taken on a ring structure with single bonds between them. I should now introduce a short a shorthand or abbreviated way of depicting organic compounds. This structure here represents cyclohexane. And so what's happening here is that each corner is a carbon. And each line between these corners is a covalent bond between adjacent carbons. The hydrogens and the structure are present but they are omitted from the shorthand structure. And so there is a carbon here. And it is bonded covalently to this carbon and that carbon. But it's also bond with violently to two hydrogens and that is emitted from the structure. So here is the ring structure cyclohexane. A ring of six carbons with single bonds between adjacent carbons and the rings. Now. Here is benzene. Benzene also has a six carbon ring structure. However, every other carbon in benzene is double bonded to the adjacent carbon that can be depicted like this, as shown here. And so rings can form when carbon skeletons maintain the rule of thumb for bonds to carbon, but close onto themselves, and so carbon skeletons may be arranged in rings, and the rings can have single or double bonds between adjacent carbons. As long as the rule of thumb for bonds to carbon is maintained.

Another phenomenon that I want to discuss with you is called isomers. Compounds can have the same formula. That is, the molecules may be made up of the same building blocks, the same atoms. But the arrangement of those atoms can be different. For example, here are what are called structural isomers. This molecule has 1234 carbons, as does this molecule. However, the arrangement of the atoms in the molecules is different and so structural isomers are rearranged. Now imagine that this were an actual model that you made on your desktop using spheres and sticks. If you were to make a model such as this or this structural isomer, what you would observe is that there would be rotation possible around this axis because the stick allows rotation. Something analogous, something similar also happens in real life. Single bonds allow a degree of movement that double bonds between carbons do not, and so the presence of double bonds between these two carbons and also these two carbons result in what are called geometric isomers. The atomic composition of this molecule is the same as that molecule. However. This arrangement and that arrangement are not the same. They are rotated and in fact you cannot rotate one to generate the other because of the presence of the double bond that tends to. So to speak. Fix the carbons in space. So these are geometric isomers. Now take a moment and look at your two hands. And imagine that your two hands are molecules. Your two hands are analogous are similar to what we would call. And then tumors and then tumors in chemistry. And then tumors are handed molecules and and tumors have the same composition of atoms. But they are arranged in a mirror image like your hands are arranged in a mirror image. Another word for an enantiomers is a chiral molecule. And so chirality reflects handedness in chemistry.

Now, the key to chemistry and understanding the structures of molecules is that the structures are tied to their function. And so organic compounds have unique properties, and those properties are dependent upon the size and shape of the carbon skeleton and the groups of atoms that are that are attached to that skeleton. This means that molecules that are very, very similar can still have different functionalities inside a living organism. Let's consider a very similar molecules, and let's look at how the differences in their structure yield differences in their function. Let's consider two sex hormones or steroids. These are called testosterone and estradiol. And I imagine many in the audience will have heard these terms before. And so the sex hormones testosterone and estradiol differ only in the groups of atoms that are highlighted in this figure. And so here is testosterone. Notice it is a molecule with a base or core structure that has a characteristic for carbon rings. This is classical steroid structure. And here is estradiol. And also here are its four carbon rings. In fact, both testosterone and estradiol are derived from are made from the same molecule inside the body. That's why they have a common basic structure. They are made from another molecule called cholesterol. Cholesterol also has this four ring structure. So how did testosterone and Astra style differ? Well, in testosterone there is this methyl group here. This three group is called a methyl group as well. And there is an oxygen here.

Notice that the oxygen has two covalent bonds to carbon here. Estradiol lacks the methyl group and has what's called a hydroxyl group here instead. So to the casual observer, these structural differences may seem minor. Given that the core of the molecule is shared between testosterone and estradiol. However, these differences suffice to give the molecules the hormones. Dramatically different effects and functionalities inside a living organism. For example, an abundance of testosterone during specific parts of embryonic. And post embryonic development in males yields. This result in lions and an abundance of estradiol correspondingly yields this result in lions. And so the core structure of testosterone and astral tail shared. They differ in this methyl group and the oxygen here versus the hydroxyl group there. But look at the differences in functionality as a result of these chemical alterations or chemical differences between testosterone and estradiol. The secret behind chemistry and biochemistry is that when you change something, you now have a different thing. And that different thing may have different functions inside a living organism.

So I mentioned some vocabulary and talked about some chemical groups, and it's worthwhile examining important chemical groups in greater detail. I mentioned the hydroxyl group O-H. This is how it is depicted. And here it is. And a two carbon molecule. This is an alcohol. So that's a hydroxyl group. Here's a carbonyl group. A carbonyl group is a carbon double bonded to oxygen shown here. It forms aldehydes or ketones in the body. This is a carboxyl group. A carboxyl group is drawn out c o o h. And it actually has this structure shown here in carboxylic acid. And this hydrogen can be lost. Chemists call that deprotonate. And it results in an ionized carboxyl group an ionized carboxyl group. Here is an amino group NH2, drawn like this. This is an amine and an amino group can actually gain.

A proton and also become ionized as shown. Here is a phosphate group. We'll talk extensively about phosphate groups because they are very versatile and they are used extensively in biochemical processes. And so a phosphate group is drawn like this. And this is its structure. This organic phosphate.

On a molecule of adenosine generates adenosine triphosphate. Adenosine triphosphate, also called ATP. And here is a methyl group. I mentioned the methyl group before. It's three. It is a carbon bond to bonded to three hydrogens. Here is a methyl group and a methylated compound. Please look through these lists of names and notations and structures so that you are familiar with the various chemical groups, because they will become very, very useful in our subsequent discussions.

The versatility and diversity of molecules produced by cells is remarkable. However, cells make all these large molecules from only a limited set of small molecules, and so there are four classes of molecules that are important to organisms that we'll discuss. Carbohydrates and lipids. Proteins and nucleic acids. And all of these complex molecular structures are made up of smaller building blocks inside cells.

So the four classes of biological molecules can contain very large molecules indeed. And so they're called macromolecules. Macro meaning large. And so they're called macromolecules due to large size. They're also called polymers because although they are large they are made up of repetitive smaller units called monomers. So the polymer is the final macro molecule. And the monomers are the individual smaller building blocks that are strung together by the cell.

And so this is a handy chart with examples of monomers and polymers. Again the monomers are the building blocks. The polymers are the large biological macromolecules. And so if the monomer is a monosaccharide mono means single and saturated means sugar. So if the monomer is a simple sugar, for example glucose or fructose, the polymer is a polysaccharide. Examples of polysaccharides are starches and glycogen and cellulose. And we'll talk about polysaccharides soon. If the monomer is an amino acid. Examples of amino acids include leucine and arginine. Then the polymer is a polypeptide or a protein. And so examples of proteins that are important inside the body include things like insulin. Insulin is a polypeptide. It is a large biological macro molecule or a protein that is made up of amino acid subunits.

If the monomer is a nucleotide, a nucleotide is made up of a sugar, a phosphate group, and a base, then the polymer is a nucleic acid. And examples of nucleic acids are molecules that are probably familiar to you, at least by name. Nucleic acids include DNA and RNA, and so DNA and RNA are nucleic acid polymers of nucleotide monomers.

Key to understanding biological macromolecules is the concept that cells make large molecules from a limited set of small molecules, and so a variety of polymers are possible from a small group of monomers. If you consider the proteins that make up your body, proteins are very diverse structurally and functionally. However, all proteins are made up of only 20 different building blocks. We call these 20 different building blocks amino acids. DNA stores and transmits the information necessary to assemble a human. And yet that molecule is made up of just four different kinds of building blocks or monomers. We call these monomers nucleotides. It's important to note also that the monomers used to make polymers are essentially universal in all life.

This universality of the building blocks of life reflects the common origin that all organisms share.

The way that biological macromolecules are assembled and disassembled. It's also conserved throughout life. And so this slide discusses the formation and breakdown of biological polymers. Consider this short polymer. Here the purple spheres represent monomers. And notice the individual monomers are now covalently bonded to one another. Notice also the presence of a hydroxyl group here. The bonded to the terminal unit in this short polymer. Here is an unlinked monomer.

And the cell will link this previously unlinked monomer to this short polymer to generate a longer polymer. The way the cell does this is called a dehydration reaction. A dehydration reaction rearranges matter and generates or frees up a molecule of water. And so this hydroxyl group and this hydrogen are combined to generate the water. And notice that now the short polymer has been elongated by plus one monomer to make a longer polymer. This is a dehydration reaction. And so dehydration reactions remove water to create longer polymers. Now cells also break down polymers into the constituent monomers. This involves hydrolysis. And water is necessary for hydrolysis. And so in the presence of a water molecule, a terminal component of a polymer is freed up to generate a free monomer and also a shorter polymer. So hydrolysis reactions break down polymers and require water, whereas dehydration reactions create polymers and remove water.

So what cells are doing is they're assembling large polymers from small building blocks, small monomers, and they break apart polymers into component monomers. Monomers are the individual subunits of polymers, and so monomers can be simple sugars. In the case of carbohydrates or fatty acids, in the case of lipids or amino acids, in the case of proteins or nucleotides, in the case of nucleic acids like DNA and RNA, and the polymers are the molecules that are made up of multiple monomer subunits, and so carbohydrates and lipids and proteins and nucleic acids are the respective polymers of the monomers that I mentioned previously.

Rearranging matter in this manner. Generating and breaking covalent bonds, as I've described, requires energy, and it also requires what we call enzymatic catalysis. These are enzyme driven reactions. Enzyme driven reactions generate large molecules from smaller subunits and break large molecules into smaller subunits. I should define the term enzyme. An enzyme is a biological molecule that acts as a catalyst. It speeds up a reaction without being itself changed by that reaction. There's a specialized term that is used to summarize all the enzyme mediated biochemistry that is hosted by an organism. That term is called metabolism. And so metabolism is the sum of all enzyme mediated reactions inside cells. The reactions can include biochemistry to acquire and use energy, to stay alive, to grow and to reproduce. So metabolism describes all the enzyme catalyzed biochemistry inside a living organism. That's what the term metabolism means. And an enzyme is a biological molecule that.

Accelerates the rate of a reaction without being changed by doing so.

The first category of biological macromolecules that we want to discuss are carbohydrates.

So monosaccharides are single, sugars are the simplest carbohydrates. And so carbohydrates range from small, simple sugar molecules or monomers to large polysaccharides. Sugar monomers are monosaccharides, such as those found in things like fructose or glucose, or in fact, honey is almost entirely sugar. Now. The carbon skeletons of monosaccharides can vary in length. Glucose and fructose are six carbon sugars, but other sugars can have 3 to 7 carbon atoms. Monosaccharides are the main fuels to run the cell, and they're also used as raw materials structurally to manufacture other organic molecules.

Monosaccharides can be linked together or hooked together by dehydration reactions described previously. And so in this way the cell can form more complex sugars and polysaccharides. Here is glucose and here is fructose. And here is the disaccharide sucrose. Sucrose is cyclic glucose linked to cyclic fructose. And so sucrose is a disaccharide with glucose and fructose monosaccharides linked together sucrose is common table sugar. So two monosaccharide monomers can form a disaccharide or a two sugar molecule. Here, two glucose molecules through a dehydration reaction, are joined together to form maltose, the disaccharide maltose, as an example. Polysaccharides are also certainly possible. Polysaccharides are macromolecules that are made up of many, many monosaccharides. Up to thousands of monosaccharides and polysaccharides have a variety of functions inside a living organism. They can be structural molecules or they can be storage molecules. An example of a polysaccharide is starch, and starch is made up of glucose monomers, and it's used by plants for energy storage. And in fact, we can digest starch when we eat those plants and break down the polysaccharide into its monomer subunits and use that as energy. Glycogen is also a polysaccharide, and it is also made up of glucose monomers, and glycogen is used by animals like humans for energy storage. There's also cellulose. You've probably heard of cellulose. It too is a polymer of glucose. Cellulose is not digestible by humans. It forms plant cell walls. and it is a very resilient physically molecule. And so it gives plants structural integrity. Chitin is a polysaccharide that you're probably familiar with indirectly because it is used by insects and crustaceans to build an exoskeleton. And so if you've ever had a crab or lobster for lunch or dinner, the hard outside shell is composed primarily of the polysaccharide chitin. Chitin is also found in the cell walls of various fungi.

Let's look at examples of polysaccharide polymers. And let's look at different molecules that all use the same monomer in their structure. Let's look at polymers of glucose. We'll look at starch glycogen and cellulose. And in fact this picture here contains all three of these polysaccharide polymers. Inside the potato are starch granules. And starch is a glucose monomer.

That is a linear arrangement of glucose molecules bonded together covalently. So this is starch and it's used by plants to store energy. We can digest starch and use it as an energy source. After we eat something that is starchy inside this person's muscle, tissues are granules of glycogen. Glycogen is used by animals to store energy. Glycogen is also a polymer of glucose. However, in glycogen there are branches to the polymer. You can see the branching here and there. And so starch is linear whereas glycogen has a branched structure whereas. Both of these polymers use the same monomer of building block glucose. They differ in the arrangement of the monomers, and so they have different physical and chemical properties as a result. Now in the plot here and also in the person's clothing, if it is a natural materials, there are cellulose. Microfibers cellulose is used by plants as a structural material, and it too is a polymer of glucose. It is a polysaccharide polymer of glucose. However, cellulose has a very robust structure physically.

That toughness, that rigidity to the structure of cellulose is due to hydrogen bonds that occur. Between adjacent polymers, strands of glucose in cellulose. And remember, hydrogen bonds are weak. However, the large number of hydrogen bonds holding the strands in cellulose together have an accumulated effect, and this accumulated effect strengthens the material significantly and allows cellulose to be used by plants for its structural integrity. So here are examples of polymers of the same monomer that have different arrangements of the monomers in their molecular structures, and as a result, have different properties.

Let's talk about lipids next. Fats are lipids that are mostly energy storage molecules, although they can have other roles in the body as well. Lipids are not soluble in water. They are what we call hydrophobic or literally water, fearing they are insoluble, not soluble in water. They're important for long term energy storage. They have a high energy content, and so they can contain twice as much energy as a polysaccharide. And they're made up mostly of carbon and hydrogen atoms linked by nonpolar covalent bonds. We'll consider three specific types of lipids in our discussion. We'll talk about fats and phospholipids on steroids. First, fats are fat is a large lipid made from two kinds of smaller molecules. These smaller molecules are glycerol and fatty acids. Here's an example of what we call adipose tissue. And so here are fat droplets inside a human cell. Here is the nucleus of the human cell. And here are a large number of droplets of fat. Each individual fat molecule is depicted here as. So this is called a triglyceride a triglyceride. Now the energy content of fats is very, very high. A gram of fat is worth twice as much energy to a human as a gram of a polysaccharide. And so humans and other organisms store fats in order to have energy reserves. But fats also have other functions inside the body. And so the kidneys are actually cushioned in um. A layer of fat to protect the organ itself, and fats also serve as thermal insulation in the body so that the body can maintain its internal heat. There's a layer of fat beneath the skin in what is called the hypo dermis. I should point something out. This is the generalized structure of a fat molecule. This is called a triglyceride. All triglycerides generally look like this. However, they do not actually polymerize. And so triglycerides can be present in very large numbers inside cells. However they do not covalently bond to one another.

You've probably heard the term fatty acid. A fatty acid links to glycerol by a dehydration reaction, and three fatty acids linked to glycerol form what is called a triglyceride. It's called a triglyceride because of its structure that includes three fatty acids bonded to glycerol. So that's what a triglyceride actually looks like. And here is a molecule of glycerol. This arrow here and there depicts a dehydration reaction that will covalently bond this fatty acid to glycerol at this position here. And two more such reactions occur to generate a triglyceride. Notice the change in the physical shape of the molecule. That is the result of a double bond in the large carbon chain and the fatty acid here. And so this double bond generates this kink in the fatty acid tail that changes the physical properties of the triglyceride. It changes how closely triglyceride molecules can actually stack or arrange themselves near one another inside a cell. And so some fatty acids contain one or numerous double bonds. We call these unsaturated fatty acids. Unsaturated fatty acids have one or more double bonds in the long carbon tails. That means that there are fewer hydrogens on each carbon of the double bond. And these double bonds cause physical kinks or bends in the carbon chain, and they prevent the molecules from packing more tightly together and solidifying at room temperature. This means that unsaturated fats tend to be light oils, whereas fats with the maximum number of hydrogens or fats lacking double bonds in the carbon tails are saturated fats. Saturated fats tend to have a higher density, and so butter and red meat are high in saturated fat content, whereas fish oils and light vegetable oils like olive oils, are high in unsaturated fat content, for reasons we'll discuss later. The body processes unsaturated fats in a manner that tends to be healthier than what happens to saturated fats.

And so unsaturated fats are oils. Animal fats are usually high in saturated molecules, and they tend to be solids. Imagine lard, which is an animal fat, versus olive oil, which is largely unsaturated fat. Now there's also another kind of fat that is made in food production industrially. And this is called trans fat. Trans fats are made by adding hydrogen atoms to liquid vegetable oils. This is done for a variety of practical and financial reasons. In the production of processed foods, however, artificial trans fats are very bad for human health. They raise cholesterol levels and they increase the risk of heart disease and also diabetes.

Next. Let's talk about phospholipids. Phospholipids are important in the structure of cell membranes. Phospholipids are the major component of all cell membranes. Structurally they are similar to fats, whereas fats or triglycerides contain three fatty acids. Attached to this are phospholipids contain two fatty acids attached to glycerol. And so here is the generalized structure of a phospholipid. Notice once again hydrophobic tails. However, these long carbon hydrogen tails are two rather than three. And the um. Head of the phospholipid molecule is actually hydrophilic. It's made up of a glycerol and a phosphate group. So here is the hydrophilic head. Here are the hydrophobic tails. Notice the double bond in this particular tail generates the now familiar kink. And so phospholipids are generally symbolized like this. And.

In order to have this molecule exist in an aqueous environment. What happens in membranes is a phospholipid bilayer is formed in the phospholipid bilayer. That is the major lipid component of membranes, such as the membranes inside human cells. There is water or an aqueous environment outside and inside the cell, and the phospholipids in the membrane arrange themselves with their hydrophobic tails facing one another and the hydrophilic heads facing the outside and the inside of the cell, respectively.

Next we'll talk about steroids. Steroids are lipids with a variety of functions. And they all share this characteristic for ring structure. And so when you see a molecule with these four rings that molecule is a steroid. Cholesterol is a steroid. And cholesterol is a common component in animal cell membranes. And it's also the building block or the starting material for the cell to make other steroids, including the sex hormones estrogen and testosterone, shown here. Notice the characteristic four ring structure that was also seen in cholesterol and is common among all steroids. Notice also the chemical structural differences between estrogen that lacks a methyl group here that is present in testosterone and has a hydroxyl group here that is not present in testosterone. An abundance of estrogen during development results in a duck that looks like this. An abundance of testosterone during development, in contrast, results in a duck that looks like that. Notice that the structure and function of biological macromolecules are tied, and what we may consider minor variations in structure can have a significant impact on the function of a molecule in the organism. Let's talk about proteins next. Proteins are involved in nearly every function of the body. These are very diverse molecules and they can be very large molecules.

And even though they can be structurally very different to one another, all proteins are made up of just 20 different amino acid monomers. Here is the generalized structure of an amino acid. And so this is the generalized structure of the monomer that makes up all the proteins in your body. There's an amino group. There's a central or alpha carbon. There's a side chain that can differ from one amino acid to the other. And there's a carboxyl group. The amino group, the central carbon and the carboxyl group are common to all amino acids. That means that what gives each amino acid its functionality and its different identity is the nature of the side chain. So the atoms that make up the side chain of each amino acid make one amino acid differ to another amino acid. Proteins are therefore polymers of these 20 different amino acid monomers. And so here is the amino group. Here's the alpha carbon. Here's the carboxyl group. These are all shared among all amino acids. But the R group is different. And because all amino acids differ in their R group, each individual amino acid may have different physical or chemical properties to contribute to the protein. Because each R group has a specific shape and a specific atomic composition. And so there are three different basic kinds of R groups. Our groups can be hydrophobic, meaning they're nonpolar. They can be hydrophilic, meaning they are polar, or in fact they can even be charged or ionized. And so here are examples of two different amino acids. Notice the core structure in leucine and the core structure in Sirin are conserved. They are the same. Where leucine and searing differ therefore is not in their core structures, but in the composition and identity of the are groups. Here is the all group of leucene. It is branched but it is composed of carbons, and so Lucene has a non-polar or hydrophobic group. In contrast, serine has a hydroxyl group in its ah group, and so serine has a polar or hydrophilic ah group.

Let's continue this train of thought and consider leucine versus serine and aspartic acid. Our groups give different characteristics to each amino acid. And so consider why leucine is hydrophobic. Leucine is hydrophobic because of the hydrophobic nature of its our group that is made up of carbon and hydrogen atoms. Serine and aspartic acid have oxygen. Here is the hydroxyl group in.

Syrians are group and. Here in aspartic acid you see essentially a carboxylic acid group. So the reason that these are groups make these amino acid serine and aspartic acid hydrophilic is because the R groups are polar. The reason this R groups makes leucine hydrophobic is because this R group is nonpolar. This means that different amino acids have different physical and chemical characteristics, because of the differences in the composition and structure of their respective R groups.

Now let's look at the various roles that proteins can play in the body. And let's look at the major types or kinds of proteins. Proteins can be structural. In other words they can provide support. An example is the protein composition of hair. The protein composition of hair gives hair its toughness. Or there are storage proteins. And so proteins can provide amino acids as building blocks for growth. And there are proteins in eggs, for example, that provide amino acids that the body can actually grow. Proteins can change shape and contract. Contractile proteins help with movement. And they are major protein components of the muscular system. And so we'll talk about muscles and how they contract using protein components later on in the course. Proteins can also act as molecular transports. These transport proteins bind specific molecules and transport those molecules in the body. They help to move other molecules. An example is hemoglobin. Hemoglobin in red blood cells helps transport oxygen. To various tissues in the body. Proteins can also have a catalytic role. When. Proteins act as biological catalysts, they are called enzymes. And so what enzymes do is they accelerate the rate of chemical reactions. And in fact, there are cleaning products and detergents that contain enzymes in order to allow them to work better, and breaking down a food that may be in our laundry and so on. Okay, now. There are other types of proteins and other mentioned transport proteins. Transport proteins may be embedded in cell membranes and move nutrients into cells. There are proteins that are components of the immune system. These defensive proteins include antibodies. There are also signaling proteins, including hormones. I mentioned insulin. Previously, insulin is a hormone signaling protein. There are also other chemical messengers in the body that are protein in nature, and there are receptor proteins that are built into cell membranes. And these receptor proteins receive and transmit signals.

On the surface of cell membranes. In order for cells to respond to those signals. So the function of different types of proteins depends on the individual shape of each protein, and the shape of each protein depends on the amino acid composition and the sequence of amino acids that make up that protein. So a polypeptide chain can contain hundreds or even thousands of amino acids that are linked by what are called peptide bonds. And this amino acid sequence causes the polypeptide to assume or to fold into a specific and particular shape in 3D space. And so here is a model of a protein folding in what is called its native conformation or its native or functional shape. And the shape dictates function and what dictates the shape the sequence of individual amino acids.

Proteins form through dehydration reactions that involve the loss of one water molecule. What happens? Is. A water molecule is lost during the dehydration reaction, and the water molecule is made up of a hydroxyl group from the C terminus or carboxyl terminus of the growing polypeptide, and a hydrogen from the amino group of the amino acid that is going to be added to the polypeptide and a new bond is formed. This new bond is called a peptide bond. A peptide bond is a kind of covalent bond, and it attaches the alpha carboxyl carbon to the next alpha amino nitrogen, and thus extends the polypeptide by a single amino acid. I should clarify that proteins have two ends the amino terminus and the carboxyl terminus. And so we use N and C or amino and carboxyl to orient ourselves on a polypeptide chain. And this polypeptide chain can be several thousand amino acids long.

Now. Proteins have specific shapes or conformations, and the functionality of each protein depends upon its specific shape or conformation. Proteins only work if they're in the right shape.

And the linear chain of amino acids that I just described has to be folded in a very specific way to give proteins their specific shape and functionality. There are four levels of protein structure primary, secondary, tertiary. And in the case of proteins that are made up of more than one polypeptide. Cautionary structure. Let's look a bit at these example proteins and talk a bit about how form follows function. Here is the influenza virus. Notice that there is a specific shape along this surface of the virus. And notice how tightly the shape of this protein which is an antibody. Matches the shape of this influenza virus. And so the antibody is a protein component of the immune system that is tasked by the body with recognizing foreign entities, including viruses. And so this antibody has to have a specific conformation in order to function. And the functionality that I'm talking about here is the recognition of the influenza virus. Here is lysozyme. Lysozyme is an enzyme. And enzymes remember our biological catalysts. And so this protein has to have a specific shape in order to bind what is called its substrate and act upon it and catalyze a reaction, in other words. And so it relies upon this conformation that generates a groove, this groove.

Is necessary for the protein for the enzyme lysozyme to have its specific functionality. Here is collagen. Collagen is a trimeric polypeptide. And so what that means is that it has three individual components, and it has to be folded in this particular shape in order to have its structural properties that are necessary for it to work. So form follows function and proteins. The primary structure of proteins is determined by the linear amino acid sequence. And so each of these spheres represents a different amino acid. Here is the amino end and here's the carboxyl end of the polypeptide. And each of these amino acids is bonded to adjacent amino acids before it and after it in the linear sequence by peptide bonds. And so here is a peptide bond. Here are various amino acids. Here is the n terminus. Here is the C terminus. And notice the backbone or core elements of the amino acids are shared. How the amino acids differ is in there are groups are side chains. Here are the peptide bonds that. Link adjacent amino acids together in the primary protein structure.

The secondary structure of proteins depends upon hydrogen bonding within elements of the backbone. And so what this does is it results in the protein folding on itself or coiling on itself, either in a helical structure called an alpha helix shown here, or in a pleated structure called beta pleated sheets shown here. And so secondary structure results when non adjacent amino acids have hydrogen bonds that form between their core elements. The r groups of amino acids are not involved in secondary structure. Instead, hydrogen bonds form between non adjacent amino acids and these hydrogen bonds form between core elements or backbone elements of these non adjacent amino acids. Remember hydrogen bonds are individually weak, but the presence of numerous such bonds can have a cumulative effect and stabilize the protein into secondary structure, either as an alpha helix or as a beta pleated sheet.

So here is a primary structure. Notice that primary structure depends on covalent bonds. Strong peptide bonds between adjacent amino acids to form a linear sequence of amino acids in the protein. Protein secondary structure can take the form of an alpha helix or a beta pleated sheet. Both these structures rely on hydrogen bonds between the backbone. Elements of non adjacent amino acids. That is they both rely on hydrogen bonds between core structural elements of amino acids that are distinct to one another.

So tertiary structure and tertiary structure is stabilized by interactions that involve non adjacent our groups. So whereas in secondary structure the groups were not involved in tertiary structure the are groups are involved. Finally if proteins have more than one polypeptide to make the final functional protein, then they also have cautionary structure. And the rules governing quaternary structure generally mirror those rules governing tertiary structure. Tertiary structure.

Can be assembled or held together using a variety of interactions. These include hydrogen bonds between our groups or hydrophobic interactions between our groups, ionic interactions between our groups, or what are called disulfide bridges. Disulfide bridges are covalent bonds between distant cysteine are groups. Cysteine is an amino acid, and cysteine are groups. Can disulfide bridge or covalently bond one another. These interactions. Can occur both within and between polypeptides and their depicted here. So here is a hydrogen bond involving the ah groups of non adjacent amino acids. Here are hydrophobic interactions involving the R groups of non adjacent amino acids. Here are ionic interactions involving the r groups of non adjacent amino acids. And here are disulfide bridges are covalent bonds between sulfur atoms. In the are groups of non adjacent amino acids. All these interactions are possible and tertiary structure relies upon these interactions. Cautionary structure occurs when two or more polypeptide chains interact, and so these proteins are oligomers of various polypeptide chains. One such trimeric protein is collagen. I have talked about collagen previously, but there's also hemoglobin. I mentioned hemoglobin for its ability to transport oxygen in red blood cells. And so hemoglobin has 1234 different polypeptide chains. And so it's a protein that has primary secondary tertiary but also cautionary structure.

So proteins have a wide range of structures and therefore a wide range of functions. However, their functionality relies upon their conformation or shape. If a protein loses its native conformation, if it is misfolded and does not have the correct shape, it can no longer function. This is a process called denaturation. In denaturation. A protein unravels, loses its specific shape, and therefore loses its function. Now various physical and chemical processes can denature proteins. Proteins can be denatured by changes in salt concentration, pH, or high heat.

And so whereas the native conformation shown here is the correct shape of a functioning protein, and a protein's functionality depends upon its native conformation. The denatured state loses the native conformation, and so the denatured state also loses functionality. When a protein unfolds, it is denatured and the denatured protein does not work, it loses its function. What can denature a protein? High salt changes and changes in temperature. The presence of detergents and also organic solvents can all denature proteins. Sometimes proteins can re nature or resume or take up once again in their native conformation. Other times this is not possible. And so the reason why a high fever, a high body temperature can be life threatening is because proteins in the body. Can denature above 40 degrees. And body temperature is normally around 37 degrees. Another example is to do with hairdressers and hairdressing, and so a perm uses high or heat to alter hair shape. By denaturing the protein components of individual hairs.

Next, let's talk about nucleic acids. Nucleotides are the monomers that make up nucleic acid polymers. This is the generalized structure of a nucleotide. And it comprises a nucleoside which is a nitrogenous base and a five carbon sugar or a pentose sugar and the phosphate group. And so each nucleotide has a phosphate group. It has a five carbon sugar called a pentose sugar and a nitrogenous base. A five carbon sugar is called a pentose, and there are two pentose sugars that I want to discuss because of their presence in nucleic acids. What is ribose shown here? And the other is deoxyribose shown here. Everywhere you see a corner in the diagram that is not labeled, that is a carbon atom. Remember there are four bonds to carbon. And so each instance of a corner here and there and there, there, there and there and so on. Those are carbons. Chemists actually number the carbons one prime two prime, three prime, four prime and five prime. And each of these five carbon sugars ribose has a hydroxyl group shown here bonded to the second carbon two prime deoxyribose as the name implies does not. Ribose is present in ribonucleic acid or RNA. Deoxyribose that lacks the hydroxyl group at C2 is present in deoxyribonucleic acid or DNA.

Now there are also five different nitrogenous bases. DNA and RNA each use four nitrogen bases. Three are shared between DNA and RNA, and the fourth differs. Nitrogenous bases are nitrogen rich molecules, and there are two molecules classified as what we call purines and three molecules that we classify as pyrimidines. The purines are common to both DNA and RNA, and they are adenine and guanine. Notice that the purines, although they have a shorter name, have a more complex two ring structure. There are three pyrimidines. Pyrimidines have a longer name, but a simpler structure because each pyrimidine is only a single ring structure. Now cytosine shown here is common to both DNA and RNA, whereas thymine is only found in DNA and uracil is only found in RNA. This means that by looking at a specific poly nucleotide sequence, one can tell whether this is DNA or RNA, because DNA will have thymine or T and RNA will have uracil or you.

The way that nucleic acids are assembled also involves dehydration reactions. However, the covalent bond that results has a different name. It's a phosphodiester bond or a phosphodiester linkage. Phosphodiester bonds occur via dehydration reactions, as shown here. And so here's the water molecule that results when this hydroxyl group and the hydrogen are combined and matter is rearranged and a new bond is formed between what are now adjacent nucleotides and a poly nucleotide chain. This linkage is called a phosphodiester linkage.

And what happens is a phosphodiester linkage links the five prime phosphate group of one nucleotide to the three prime hydroxyl group of what will become the adjacent nucleotide.

Now. DNA is a polymer of nucleotides, and these nucleotides are arranged in two strands. And so each DNA strand has two distinct ends, a five prime end and a three prime end. The five prime end has the terminal nucleotide with a three phosphate group, and the three prime end has the terminal nucleotide with a three hydroxyl group, and the width of the strands of DNA are arranged is antiparallel, and so the strands never cross, and one strand runs five prime to three prime in one direction. The other strand runs five 1 to 3 prime in the other direction. This gives these nucleotide polymers a backbone of sugar phosphate units and nitrogenous bases that essentially act as molecular appendages of sorts. The pyrimidines and purines stick out to one side of each strand in DNA. This strand and that strand are what we call complementary. In other words, wherever there is a C on this strand, there is a G on the other strand. And whenever there is an A on this strand, there is a T on the other strand. The two strands are held together. By numerous hydrogen bonds between complementary nucleotides on each of the strands, and so each C on one strand is bonded with three hydrogen bonds to a complementary G on the other strand, and each T on one strand. Is bonded to with two hydrogen bonds to an A on the other strand. This has specific implications and results. For example, a nucleotide sequence, a DNA sequence that is double stranded and GC rich would take more energy to denature than in a T rich DNA sequence. This is because there are three hydrogen bonds between every G and C in the two strands, versus only two for every A and T in the two strands.

Nucleic acids and cells store and transmit hereditary information. DNA is a data storage molecule, and the data is the instructions necessary to assemble proteins and run the cell. And so what happens is the DNA inside the nucleus of the cell contains the information that is transcribed to an mRNA molecule in the nucleus. And so this mRNA molecule contains a copy of the information. And that information is interpreted in the cytoplasm where structures called ribosomes read the hereditary information in an mRNA molecule and use it to assemble a protein or a polypeptide.

In genetics, any change in DNA sequence is called a mutation. Mutations can have no effect on the final protein. In some instances, mutations can be beneficial to the organism that bears that mutation. In other instances, mutations can be very harmful to the organism that bears that mutation. And so let's look a bit at what happens when DNA goes wrong. These are instances of heritable diseases because the issue causing the disease is encoded in an organism's DNA. And so one such disease is sickle cell anemia. Sickle cell anemia is caused by a single nucleotide mutation in DNA. That single nucleotide mutation in DNA results in a single nucleotide change in the resulting messenger RNA. That in turn results in a single amino acid change in the protein. However, that single amino acid change is what we call non-conservative. In other words, the amino acid that should be there has an R group that is chemically and physically very different to the R group of the mutated amino acid.

Here is the sequence of normal hemoglobin. And so it has a specific primary structure. And that primary structure results in a secondary and tertiary structure and cautionary structures that allow the red blood cell to function and to have the correct shape, because the hemoglobin inside functions and has the correct shape as a correct coordinate structure and secondary tertiary structures as a result of the correct primary structure. And so what is the functionality of hemoglobin? Well, it transport oxygen. And to do so the molecules do not associate with one another. Instead they bind oxygen and allow erythrocytes, red blood cells, to transport oxygen throughout the body. Because the cells have the correct shape and the cells have correctly folded hemoglobin inside, a single mutation or change in the DNA sequence results in a substitution of a valine at position six. In hemoglobin, this means that the secondary, tertiary, and cautionary structures of hemoglobin are affected, and they are affected in a way that prevents hemoglobin from assuming its correct conformation. This means it has the wrong shape and it cannot work. For one, the hemoglobin molecules tend to associate with one another, and this results in hemoglobin crystallizing inside the cells and forming these fibrous structures and. That deforms the entire red blood cell and gives it the sickle like shape. Also, these mutant hemoglobin molecules cannot effectively bind oxygen, and so the loss of their conformation results in hemoglobin molecules that lose their functionality. And sickle cell anemia is a terrible disease. As a result, because patients have poorly formed and poorly functioning red blood cells, they cannot transport oxygen to their tissues. And so they have a series of very serious health problems as a result.

A key concept in all biology is what we call the central dogma. The central dogma of biology describes the flow of information inside the cell, and the flow of information inside the cell is from DNA to RNA to protein. That is to say, DNA is transcribed into an RNA molecule that is translated into a protein. What life is doing is using one kind of polymer to store and transmit the information necessary to generate a different kind of polymer. So poly nucleotides, nucleic acids are used as information storage and transmission molecules in order to assemble a polypeptide that will become a protein made up of amino acids. DNA does not build proteins directly. RNA is a molecular intermediary into which DNA is transcribed, and so the information from DNA is copied or transcribed to an RNA molecule, and that copy of the information is used on ribosomes to generate a protein through a process called translation. In eukaryotes, transcription and translation are physically separated. Transcription is done in the nucleus. Translation and the assembly of proteins is done in the cytoplasm.

So the amino acid sequence of a protein or a polypeptide is contained in a segment of DNA, and that segment of DNA is called a gene. A gene is the minimum unit of heredity. Genes are made up of DNA, a type of nucleic acid, and DNA is passed on from generation to generation. And so your DNA was inherited from your parents. And the DNA contains information and directions to copy itself and also to run the cell. It runs the cell by directing the synthesis of proteins. And so here is a gene which is a length of double stranded DNA that is sufficient to encode a protein. And so. That information is transcribed into a single stranded RNA molecule called a messenger RNA, and that information is then translated into a protein. Notice what the cell is doing. It's using one kind of polymer, one kind of biological macro molecule, a nucleic acid, to store and transcribe the information necessary to assemble a different polymer, a different biological macro molecule, a protein. The monomers in DNA and RNA are nucleotides. The monomers and proteins are amino acids. The sequence of nucleotides in the DNA tells the cell which amino acids, and in which sequence to use to assemble a protein.

So nucleic acids are polymers of nucleotides, and RNA is usually a single strand. DNA is double helical. It is a double helix in which the two nucleotide strands wrap around each other and associate with one another using base pair complementation that's shown here, and so every T on one strand binds an A on the other, and every C on one strand binds a G. Any other how with hydrogen bonds. And so the double stranded DNA molecule fold into a double helix shown here.