Biochemistry from chem for NA.docx

Biochemistry WHY THIS MATTERS: A NURSE ANESTHETIST’S VIEW Biochemistry has many applications in anesthesia. Some drugs exist as enantiomers, with left-handed (R+) and right-handed isomers (S−). In general, the R-isomer is more physiologically active. Many anesthetic drugs are equal mixtures of R (+)...

Biochemistry WHY THIS MATTERS: A NURSE ANESTHETIST’S VIEW Biochemistry has many applications in anesthesia. Some drugs exist as enantiomers, with left-handed (R+) and right-handed isomers (S−). In general, the R-isomer is more physiologically active. Many anesthetic drugs are equal mixtures of R (+) and S (−) isomers, yielding a racemic mixture (bupivacaine and thiopental). The stereoisomers may have different pharmacodynamics and pharmacodynamic actions. In some cases, one isomer leads to the desired therapeutic action, whereas the other isomer may be the cause of the side effects of the drugs. In some cases, attempts are made to create a pure R (+) or S (−) isomer in an attempt to reduce negative side effects. Etomidate is a pure R (+) isomer. An example of an anesthetic available in different forms is bupivacaine, a racemic mixture of R and S isomers, with different therapeutic effects. Levobupivacaine and ropivacaine are pure S (−) isomers with lower incidence of side effects. Ketamine is a racemic mixture of isomers in the United States, but it is available as an S (+) isomer in Europe, with more potency and fewer side effects. images BIOMOLECULES Biochemistry is the study of the chemistry that occurs in living systems, and it focuses on the biomolecules that are the building blocks of living organisms. Biomolecules are organic molecules that (roughly) fall into four categories. Each class serves one or more physiological purposes and is categorized largely on the basis of its organic functional groups. First are the carbohydrates or sugars. Carbohydrates are ketones or aldehydes that also contain multiple alcohol groups. Carbohydrates are used primarily for energy storage and structure (at least in plants and insects). Proteins are polymers of amino acids, which contain, not surprisingly, an amine functional group and a carboxylic acid functional group. These two functional groups are condensed into amide functional groups that knit the amino acids into a polypeptide chain (also known as a protein). Proteins serve as structural elements in animals and, more critically, as chemical catalysts called enzymes that make life possible. Nucleic acids are polymers of sugars, joined together by phosphate ester linkages, which contain aromatic amines whose shape forms the chemical genetic code through hydrogen bonding. Nucleic acids are the architects and construction contractors of proteins. Finally, lipids are the very diverse group of biomolecules that are characterized by a physical property rather than a characteristic organic functional group. Lipids are biomolecules that are more soluble in organic solvents, such as ether, than in water. Lipids are largely composed of nonpolar hydrocarbon functional groups, in addition to a small proportion of polar functional groups (primarily alcohols, ethers, esters, and ketones) that establish the form and function of the molecule. images CARBOHYDRATES Carbohydrates (or sugars) were originally believed to be “hydrates of carbon,” because they have the general formula Cx(H2O)y. We now know that carbohydrates are polyalcohol aldehydes or ketones. Carbohydrate names are largely based on trivial names, rather than systematic names generated by International Union for Pure and Applied Chemistry (IUPAC) rules. However, most carbohydrate names end in “ose.” There are several useful ways to categorize carbohydrates. Monosaccharides are sugars that cannot easily be broken down into simpler sugars. Glucose is by far the most common monosaccharide. The alcohol and aldehyde or ketone functional groups in monosaccharides can be used to join simple sugars into more complex structures by forming acetal or ketal functional groups. Disaccharides are composed of two monosaccharides joined by an acetal or ketal linkage. Sucrose, or table sugar, is a very common disaccharide composed of glucose and fructose. Polysaccharides are chains composed of many (hundreds or thousands) monosaccharide units. Polysaccharides include starches and cellulose. We can also classify monosaccharides on the basis of the number of carbon atoms they contain. Trioses have three carbon atoms, tetroses have four, pentoses have five, and hexoses have six. Sugars that contain an aldehyde functional group are called aldoses, and sugars that contain a ketone functional group are classified as ketoses. Aldehyde functional groups are composed of a carbon atom with a double bond to an oxygen atom and a single bond to a hydrogen atom. To simplify drawing the structures of sugars, the aldehyde functional group is often shown as CHO. For example, ribose is an aldopentose and fructose is a ketohexose (Figure 12.1). images Figure 12.1 Aldoses and Ketoses images FISCHER PROJECTIONS Most of the carbon atoms in sugars have a tetrahedral geometry. Therefore, sugar molecules are not flat but have a three-dimensional structure. The three-dimensional structure of carbohydrates is commonly depicted using Fischer projections, named in honor of Emil Fischer. Fischer worked out the structures of most of the carbohydrates in the first part of the 20th century with little technology but a great deal of genius. In a Fischer projection, you imagine the main carbon skeleton to be vertical with the carbon–carbon single bonds rotated so that the carbon chain is curved out toward you (Figure 12.2). images Figure 12.2 Fischer Projection of Glyceraldehyde Let’s take a look at glyceraldehyde. From the viewer’s perspective, the aldehyde carbonyl group (CHO) points up, and the CH2OH group points down. The OH group points to the viewer’s right, and the H points to the viewer’s left. Therefore, the Fischer projection puts each of these groups in that orientation. It is important to recognize that, although a Fischer projection is drawn in the plane of the page, it represents a three-dimensional molecule. The horizontal bonds are projected toward you and the vertical bonds are projected away from you. Chirality Chirality is a topological property of an object, and an object is chiral if it is different from its mirror image. The word “chiral” comes from chiros, the Greek word for “handed.” Since chiral has a Greek origin, it is pronounced with a hard ch, such as “kiral,” not “shiral.” For example, your right and left hands are mirror images of each other, but they are not identical. So, your hands are chiral. Socks are not chiral, so there are no left-handed socks and right-handed socks. Molecules can also be chiral, and this subtle difference is crucially important in the world of biochemistry. Many molecules—especially biomolecules—are chiral. A molecule is chiral if there is a “righthanded” form of the molecule that is different from a “left-handed” form. The right-handed and left-handed forms1 are called enantiomers. Enantiomers are mirror images of each other, but they are different compounds, even though they have identical formulas and identical atom connectivity. Enantiomers have identical chemical and physical properties, except for how they interact with other chiral molecules and how they interact with plane-polarized light. You already have experience with how chiral objects interact with other chiral objects. Your right hand interacts differently with right-handed gloves and left-handed gloves. The same is true for chiral molecules. We explore the interaction of chiral molecules with polarized light in the “Optical Activity” section. Carbohydrates belong to the right-handed family, and amino acids belong to the left-handed family. In general, our bodies can use only one of the handed isomers of a chiral molecule. Introducing the wrong-handed isomer can have effects ranging from amusing to a noneffect to disastrous. For example, the right-handed isomer of carvone smells like spearmint, while the left-handed isomer smells like caraway. Underground chemists have learned that the pure left-handed isomer of methamphetamine is much more potent than a mixture of the two isomers. Presumably, our bodies simply ignore the right-handed isomer. The antinausea drug thalidomide was once prescribed to fight morning sickness during pregnancy. The correct-handed isomer did indeed reduce morning sickness. However, the wrong-handed isomer caused horrific birth defects known as thalidomide babies. In order for a molecule to be chiral, a molecule must contain one or more stereocenters.2 A carbon is a stereocenter when it has four different groups. Notice we didn’t say “chiral carbon,” because chirality is a property of the molecule as a whole and is not localized on any single atom or group of atoms. Let’s take a look at glucose and decide which carbons are stereocenters (Figure 12.3). images Figure 12.3 Stereocenters in Glucose The C1 carbon (the carbonyl carbon) in glucose is not a stereocenter. Yes, it does have a total of four bonds, but it has bonds to only three different groups: the oxygen, the hydrogen, and the next carbon in the chain. The bottom carbon is also not a stereocenter, because the carbon is bonded to a carbon group, an OH group, and two identical H atoms. In order to be a stereocenter, the carbon must be bonded to four different groups. All of the other carbons in glucose are stereocenters. For example, C2 has bonds to an OH group, an H, the aldehyde functional group, and the rest of the chain. C3 has bonds to an OH group, an H, a two-carbon group above, and a three-carbon group below. Notice we said stereocenters have bonds to four different groups, not four different kinds of atoms. There are several conventions to indicate the configuration of a stereocenter. The most precise is the IUPAC system that names the configuration around a stereocenter as R (for right handed; rectus) or S (for left handed; sinister). You have probably seen the R/S descriptors on drug information sheets. The details of the R/S system are beyond our purposes here, but any standard organic chemistry text will discuss how to assign these descriptors. Optical Activity One cool property of the chiral molecules is optical activity. Enantiomers of a chiral molecule interact with polarized light, but one enantiomer tilts the polarization in one direction, while the other enantiomer tilts it in the opposite direction. This phenomenon is called optical activity. Light is called electromagnetic radiation because it can be described by an electric field and a magnetic field (Figure 12.4). These two fields oscillate like waves, at right angles to each other and to the direction in which the light is traveling. These fields can oscillate in any direction as long as they are at right angles to each other. If you imagine the light is heading away from you, you could observe the electric field to be oscillating up and down, or left to right, or at any intermediate orientation. images Figure 12.4 Electric and Magnetic Fields of Light You get polarized light by passing regular (unpolarized) light through a polarizing filter, which allows oscillation of the electric field only in one plane. When polarized light passes through a sample of a chiral (nonracemic) material, the orientation of the polarized light is rotated (Figure 12.5). images Figure 12.5 Rotation of Plane-Polarized Light by a Chiral Sample Enantiomers that rotate polarized light in a clockwise direction (to the right) are called the dextrorotatory isomer and labeled as the (+) enantiomer. The enantiomer that rotates polarized light in a counterclockwise direction (to the left) is called the levorotatory isomer and is labeled as the (−) enantiomer. A solution of glucose rotates polarized light to the right, and this is why glucose still has a trivial name of dextrose. Fructose rotates polarized light to the left and was formerly known as levulose. A racemic mixture contains equal amounts of the (+) enantiomer and the (−) enantiomer and has the designation (±). Racemic mixtures are not optically active because the rotation of the dextrorotatory enantiomer cancels out the rotation of the levorotatory enantiomer. Synthesis or isolation of a single enantiomer in the laboratory is a challenging task, and most syntheses of chiral molecules result in a racemic mixture containing both enantiomers. The Food and Drug Administration (FDA) policy statement drafted in 1992 and updated in 20053 requires pharmaceutical companies to characterize the properties of single enantiomers, and this adds difficulty, time, and expense to the development of new medicines. D-Sugars and L-Sugars When glyceraldehyde is drawn as a Fischer projection, the OH group on the stereocenter points to the right (Figure 12.6). images Figure 12.6 D-Glyceraldehyde Emil Fischer called this the D-isomer. It turns out that virtually all naturally occurring monosaccharides have the hydroxyl group on the next-to-last carbon atom pointed to the right (when drawn as a Fischer projection). So, all naturally occurring sugars belong to the D-family. To decide which family a sugar belongs to, first draw the molecule as a Fischer projection with the aldehyde or ketene functionality at the top of the structure. Then look at the OH group on the next-to-bottom carbon. If that OH points to the right, the sugar is a D-sugar. If the OH points to the left, it is an L-sugar. Figure 12.7 shows the D- and L-isomers of glucose. Notice that the D- and L-isomers are mirror images of each other. Therefore, D- and L-isomers are enantiomers. Both compounds have some OH groups that point to the left and other OH groups that point to the right. However, in determining which structure is the D-sugar, you only consider the next-to-bottom carbon (shown in blue). images Figure 12.7 D-Glucose and L-Glucose The D-Aldohexoses Figure 12.8 shows the structures and names of the D-aldohexoses. These compounds all have six carbon atoms, an aldehyde functional group, and the OH group on C5 pointed to the right. Of these eight compounds, glucose is by far the most common. images Figure 12.8 The Aldohexose Family of Sugars Fructose Fructose is the most common ketohexose. The structure of fructose is very similar to that of glucose. The functional groups on C1 and C2 are simply reversed (Figure 12.9). D-Aldopentoses The D-aldopentoses are five-carbon sugars. The most important of these are ribose and deoxyribose because they are used to construct the nucleic acids ribonucleic acid (RNA) and DNA. Figure 12.10 gives the names and structures of the D-aldopentoses. images Figure 12.9 D-Glucose and D-Fructose images Figure 12.10 The Aldopentose Family of Sugars A Mnemonic to Learn the Structures of the Aldose Sugars Many students use the mnemonic device “All Altruists Gladly Make Gum in Gallon Tubs” to learn the names of the aldohexoses, coupled with drawing eight “blank” Fischer projections and then following a pattern of putting all hydroxyl groups on C5 on the right, then alternate by fours on C4, by twos on C3, and by ones on C2. This technique works, but it is not particularly convenient or efficient to identify the structure of a single aldohexose without drawing all eight isomers. In a system consisting of multiple components, each of which is restricted to one of two states, an effective method for enumerating all of the possible configurations is to count the possibilities using the binary number system. Starkey reported a strategy for using the binary number system to describe the structures of the aldohexoses.4 Hydroxyl groups on stereocenters that point to the right are a “zero,” and those that point to the left are a “one.” If we assign C2 as the 20 (or 1), C3 as 21 (or 2), and C4 as 22 (or 4), we can count off the sugars in the mnemonic in the order shown in Table 12.1. Although this approach has an interesting theoretical foundation, its application lacks a fundamental simplicity. However, we note that aldohexoses have four stereocenters, and the human hand has four fingers (and a thumb, of course). We can map each finger to the positions of the hydroxyl groups. Hold your open right hand in front of you, with your thumb pointing up and your fingers projected horizontally out to the left. Each finger can either be extended (pointing to the left) or closed (pointing to the right). Your index finger corresponds to the hydroxyl group on C2, your middle finger to the hydroxyl group on C3, your ring finger to the hydroxyl group on C4, and your pinky to the hydroxyl group on C5. Since C6 is not a stereocenter, it makes no difference where it is projected, so we don’t need a finger to account for its spatial orientation. Table 12.1 BINARY CODE FOR THE D-ALDOHEXOSES images Now, let’s learn to count from 0 to 7 in base 2. The index finger corresponds to 20 (or 1), the middle finger to 21 (or 2), the ring finger to 22 (or 4), and the pinky to 23 (or 8). It might be helpful to write the value on the pad of each finger (where the “fingerprint” is). When the finger is extended, you can see the number, and it is counted. When the finger is closed, you can’t see the number, and the value is ignored. For example, when all the fingers on your hand are closed, you see no numbers, and the value is zero. If you extend your index and middle fingers, you can see the “1” and the “2,” for a total value of three. A value of six requires extending the middle and ring fingers, while keeping the index and pinky fingers in the closed position (Figure 12.11). The order of the mnemonic is fundamentally based on a binary strategy. The first sugar, allose, corresponds to a value of zero, altrose to a value of one, and so forth. Holding your right hand in front of you, with your thumb pointing upward and all your fingers in the closed position, gives the binary value of zero. Where are all of your fingers pointed? They are all pointed to the right, and every hydroxyl group in the Fischer projection of allose is pointed to the right. Altrose is the next sugar in the mnemonic, corresponding to one, which means extending your index finger. Now your fingers, from index to pinky, point left, right, right, right, respectively, as do the hydroxyl groups in altrose. Glucose is the next sugar in the mnemonic and corresponds to the binary value of two. Glucose, in the form of cellulose and other polysaccharides, accounts for the majority of the biomass on this planet and is arguably the most important of all organic compounds. It is amusing to note that glucose requires a finger combination best not displayed in public. Figure 12.11 gives the structures of the aldohexoses next to the corresponding binary-finger values. To access the structure of any aldohexose, one simply says “All (0); Altruists (1); Gladly (2); Make (3); Gum (4); in (5); Gallon (6); Tubs (7)” while counting through the binary-finger values. When the desired sugar name is reached, the positions of the fingers indicate in which direction the hydroxyl groups point for that particular sugar. images Figure 12.11 Binary Mnemonic for D-Aldohexoses A nice feature of this method is that it is easily applied to other aldose systems and to the L-family of sugars. The aldopentoses are given by the mnemonic “Ribs Are eXtra Lean.” While not factually correct, this phrase corresponds to the sugars ribose, arabinose, xylose, and lyxose, and the binary values of zero, one, two, and three, respectively. To access the structures of the L-family of sugars, just use your left hand. Cyclic Structures of Sugars Monosaccharides have multiple alcohol functional groups and either a ketone or an aldehyde functional group. As we saw in the previous chapter, aldehydes react with alcohols to form hemiacetals, and ketones react with alcohols to form hemiketals. When this intramolecular reaction occurs, the linear monosaccharide forms a cyclic structure. Generally, cyclization reactions favor formation of five-membered or six-membered rings because these ring sizes are the most stable. Formation of a hemiacetal or a hemiketal is especially favorable when the reacting functional groups are contained in the same molecule. Therefore, monosaccharides exist almost exclusively as cyclic hemiacetals and hemiketals. The cyclic structures are called Haworth projections. In a Haworth projection, the lower horizontal bond in the ring is understood to be projected toward you, above the plane of the page. This bond is usually in boldface. The upper horizontal bond is understood to be projected away from you, behind the plane of the page. Let’s take a look at glucose. The Fischer projection of glucose is shown in Figure 12.12. Remember, in a Fischer projection the carbon skeleton is curved out toward you. Now, let’s rotate the Fischer projection clockwise 90°. Carbon 1 and carbon 6 are labeled to help you keep track of which carbon is which. Now, if the hydroxyl group on carbon 5 attacks the carbonyl carbon, we get a six-membered ring, as shown in Figure 12.13. The hemiacetal functional group is shown in blue. When a monosaccharide forms a cyclic hemiacetal (or hemiketal), the carbonyl carbon becomes a stereocenter. Thus, cyclization leads to formation of two possible stereoisomers. These isomers are called anomers, and the former carbonyl carbon is called the anomeric carbon. The isomer with the anomeric OH (shown in blue) pointed down is the alpha anomer. The isomer with the anomeric OH (shown in blue) pointed up is the beta anomer (Figure 12.14). images Figure 12.12 Relating Fischer Projection to Haworth Projection images Figure 12.13 Cyclization of Glucose to Glucopyranose images Figure 12.14 Anomers of Glucose A six-membered cyclic sugar is called a pyranose. Glucose is almost always found as a pyranose ring system and is formally named glucopyranose. A five-membered cyclic sugar ring is called a furanose. Fructose prefers a furanose ring system and is formally named fructofuranose. Like glucose, fructose can cyclize and can form either an alpha anomer or a beta anomer. Notice that, with fructose, the anomeric identity is determined by the direction the hydroxyl group points. The anomers of fructose are shown in Figure 12.15. Glycoside Bonds We saw in the previous chapter that aldehydes react with alcohols to form hemiacetals, and hemiacetals react with another alcohol to afford acetals. Well, the intramolecular reaction of the aldehyde carbon of an aldose monosaccharide with one of the hydroxyl groups in the same molecule affords a cyclic hemiacetal. An intermolecular reaction of this hemiacetal with the hydroxyl group of another sugar molecule provides an acetal functional group. This kind of acetal linkage connects monosaccharides into polysaccharides. Biochemists refer to these acetal (and ketal) bonds as glycoside bonds. images Figure 12.15 Anomers of Fructose Glycoside bonds can be alpha or beta. Generally, we can digest only sugars that are connected by alpha glycoside bonds. Figure 12.16 illustrates the formation of an alpha glycoside bond. Notice that, in the product disaccharide, the linking oxygen atom (shown in blue) is pointed down, relative to the glucose residue on the left. Therefore, this linking oxygen atom is in the alpha position, and this is an alpha glycoside bond. The residue on the right still has a free anomeric hydroxyl group that can be either alpha or beta. The squiggly line means that either we are not specifying which anomer is present or that both anomers are present. images Figure 12.16 Formation of an Alpha Glycoside Bond Figure 12.17 illustrates the formation of a beta glycoside bond. Again, the anomeric hydroxyl group on the glucose residue on the right can be either alpha or beta. In the product disaccharide, the linking oxygen atom (shown in blue) is pointed up, relative to the glucose residue on the left. Therefore, this linking oxygen atom is in the beta position. It is irrelevant that this oxygen is pointed down, relative to the glucose on the right, because glucose on the right contributed a regular alcohol functional group in forming the acetal link, not the hemiacetal functional group. images Figure 12.17 Formation of a Beta Glycoside Bond Some Common Disaccharides Disaccharides are composed of two monosaccharides joined by a glycoside bond. Figure 12.18 gives the structures of some common disaccharides. Maltose, or malt sugar, is formally named α-D-glucopyranosyl [1↔4] β-D-glucopyranose. This name makes more sense if we break it into its components. α-D-glucopyranosyl means that the first residue is a glucose molecule cyclized into a six-membered ring, and the oxygen on the anomeric carbon is in the alpha configuration. [1↔4] means the glycoside bond is between carbon 1 on the first residue and carbon 4 on the second residue. β-D-Glucopyranose means the second residue is a glucose molecule cyclized into a six-membered ring, and the oxygen on the anomeric carbon is in the beta configuration. images Figure 12.18 Some Common Disaccharides Cellobiose contains two glucose molecules joined by a beta glycoside bond and is formally named β-D-glucopyranosyl [1↔4] β-D-glucopyranose. Lactose contains a galactose residue joined by a beta glycoside bond to a glucose residue. Sucrose contains an alpha glucose joined to a beta fructose. Sucrose differs from the other examples because the glycoside bond connects the anomeric carbon of both sugar residues. The formal name of sucrose is α-D-glucopyranosyl [1↔2] β-D-fructofuranoside. Polysaccharides Two common polysaccharides are starch and cellulose. Both are polymers of glucose. Cellulose (Figure 12.19) is the structural material in plant matter and the major component of dietary fiber. Cellulose is poly [1↔4] β-glucose. The glycoside bonds in cellulose are beta. This configuration allows cellulose to adopt a fairly linear conformation, with a great deal of hydrogen bonding. This is part of the reason that cellulose is such a strong material. images Figure 12.19 Cellulose Starch (Figure 12.20) is a polymer of glucose that we can digest. Starch is poly [1↔4] α-glucose. The glycoside bonds in starch are alpha. This configuration puts a bend in the chain. In fact, starch adopts a helical conformation. images Figure 12.20 Starch Chains of starch molecules can branch by forming [1↔6] glycoside bonds, as shown in Figure 12.21. This branching leads to more compact forms of starch, such as glycogen and amylopectin. images Figure 12.21 [1↔6] Branching in Starch images LIPIDS While the other classes of biological molecules are characterized by structural features, lipids share a common physical property. Lipids are hydrophobic substances that are more soluble in organic solvents such as ether than in water. Lipids serve a myriad of biological purposes ranging from energy storage to sending chemical signals (both within an individual and between individuals), as well as serving as the main structural component of cell membranes for all living organisms. Lipids can be divided into two broad categories. The saponifiable lipids include triglycerides, waxes, and phospholipids. The nonsaponifiable lipids include steroids, prostaglandins, and fat-soluble vitamins. Glycerides Glycerides are esters composed of glycerin (1,2,3-propantriol) and fatty acids. Triglycerides have three fatty acid residues esterified to the glycerin backbone. Triglycerides are also known as triacyl glycerols. Mono- and diglycerides are mono- and diesters of one or two fatty acids and glycerin. Fatty Acids Fatty acids are long-chained carboxylic acids. Although their name includes the word “fatty,” fatty acids are not the same as fats. Fats are triglycerides and fatty acids are one component of triglycerides. Naturally occurring fatty acids always have an even number of carbon atoms. Saturated fatty acids have carbon chains that contain only carbon–carbon single bonds. Unsaturated fatty acids have carbon chains that contain at least one carbon–carbon double bond. Monounsaturated fatty acids have one carbon–carbon double bond in the chain, and polyunsaturated fatty acids have two or more double bonds in the carbon chain. Naturally occurring unsaturated fatty acids have the cis double-bond configuration. Figure 12.22 gives the most common saturated fatty acids. The IUPAC names are given first. For dodecanoic acid, C12H24O2, the parent chain has 12 carbons (do = 2 + deca = 10). The common names of the fatty acids are roughly derived from fats and oils that are rich in that fatty acid. For example, palm and palm kernel oils are rich in palmitic acid. Beef tallow is rich in stearic acid. Although stearic sounds a little bit like “steers,” it is derived from the Greek word for tallow. images Figure 12.22 Saturated Fatty Acids Figure 12.23 presents three common unsaturated fatty acids. Notice that the configuration of the double bonds is cis. The delta nomenclature indicates the position of the double bond relative to the carboxyl group. The carbonyl carbon is carbon number one. For linoleic acid, Δ9,12 octadecadienoic acid, there are 18 carbons, and the double bonds begin on carbons 9 and 12. Linoleic and gamma linolenic acids are also classified as omega-6 fatty acids. The omega carbon is the last carbon in the chain. Omega-6 indicates there is a double bond six carbons from the end of the chain. images Figure 12.23 Unsaturated Fatty Acids Triglycerides Structurally, triglycerides are tri-esters of glycerol (also known as glycerin or 1,2,3-propantriol) and three fatty acids. Figure 12.24 gives the structure of a generic triglyceride. The glycerol backbone is shown in blue. Notice that the three fatty acid chains (R1, R2, and R3) are not necessarily the same. Triglycerides are more commonly called fats or oils. A fat is a triglyceride that comes from animal sources, has a higher percentage of saturated fatty acids, and is a solid at room temperature. An oil generally comes from plant sources, contains a larger percentage of unsaturated fatty acids, and is a liquid at room temperature. Fats and oils are not pure substances, because in a given sample of a fat or oil the identity of the R groups is not the same in all molecules. For example, most of the fatty acid residues in a sample of olive oil are oleic acid (ca., 70%) and palmitic acid (ca., 10%), along with smaller amounts of linoleic acid, stearic acid, and linolenic acid. However, the fatty acid composition on a given olive oil molecule is essentially a random selection from these choices of fatty acids. images Figure 12.24 A Generic Triglyceride Figure 12.25 shows space-filling models of tristearin and triolein. Tristearin is a triglyceride containing three stearic acid residues and represents a generic fully saturated triglyceride. Triolein is a triglyceride containing three oleic acid residues and represents a generic unsaturated triglyceride. The geometry of these models was optimized using a molecular mechanics program that treats each chemical bond as a spring and each atom as a ball, and jiggles the whole model until the energy of the system is minimized. The hydrogen atoms in each model are omitted for clarity. The three carbons in glycerol are colored blue, and the oxygen atoms are red. Notice that the cis double bonds in triolein impose an awkward kink in the molecule, and this hinders triolein in settling into the solid state. The more symmetrical tristearin fits more easily into a crystalline lattice and has greater access to intramolecular London forces, and, therefore, is a solid at room temperature. images Figure 12.25 Three-Dimensional Structures of Tristearin and Triolein Saponification Since triglycerides are esters, they undergo the same kinds of reactions as other esters. One important reaction is hydrolysis by aqueous sodium hydroxide, which is a reaction called saponification (see Figure 12.26). Saponification means “soap forming,” and this is how soaps are synthesized. Hydrolysis of a triglyceride (with hot, aqueous NaOH) gives glycerin and three fatty acids. Since the reaction medium is strongly basic, the fatty acids are present in their conjugate base form. We have already discussed the function of soaps and other surfactants. images Figure 12.26 3-Saponification of a Triglyceride Detergents are synthetic soaps. Like soaps, detergents have a long, nonpolar tail and a polar head. The polar head can be anionic, cationic, or neutral. Most detergents are derived from triglyceride sources. Sodium dodecyl sulfate (SDS) is a typical anionic detergent. SDS is also known as sodium lauryl sulfate, because the carbon chain is synthesized from lauric acid. SDS is the active ingredient in laundry detergents such as Tide. SDS is shown in Figure 12.27. images Figure 12.27 Sodium Dodecyl Sulfate SDS has several advantages over soap. Unlike the carboxylate anions in soap, the dodecyl sulfate anion does not form insoluble precipitates with hard-water ions (e.g., Ca2+), leading to the formation of soap scum. Also, the dodecyl sulfate anion is the conjugate base of a very strong acid (H2SO4). Therefore, SDS is a weak base, and solutions of SDS are pH neutral. Phospholipids Phospholipids are similar in structure to the glycerides, except that one of the fatty acid residues has been replaced by a phosphate ester group. Phospholipids are common in cellular membranes because of their surfactant properties. They have long, greasy tails that are hydrophobic. The polar phosphate group, or groups bonded to the phosphate group, are hydrophilic. Thus, phospholipids can form barriers to separate the aqueous cytoplasm from the aqueous extracellular fluid while facilitating the transport of ionic and polar materials through the membrane. Phosphatidylcholine, also known as lecithin, is a typical phospholipid (Figure 12.28). images Figure 12.28 Phosphatidylcholine Steroids Steroids are characterized by the cyclopentanoperhydrophenanthrene ring system, which consists of three six-membered rings fused to a five-membered ring (Figure 12.29). Steroids play a variety of roles in living systems. Some common steroids include cholesterol, estrogen, and testosterone. images Figure 12.29 Steroid Ring System Cholesterol is an essential component of cellular membranes. In addition to dietary sources, we can also synthesize cholesterol. Cholesterol is transported in the blood as a lipoprotein, which is an aggregate of water-soluble proteins, cholesterol, and other lipids, including triglycerides. Proteins are denser than lipids, so the ratio of protein to lipid determines the classification of the lipoprotein. High-density lipoproteins (HDL) have a greater protein-to-lipid ratio than low-density lipoproteins (LDL). Thus, from a chemical standpoint, there really aren’t “good cholesterol” and “bad cholesterol.” High levels of LDL are indicative of potential heart problems, not because of a different form of cholesterol, but because LDL particles are more likely to dump their load of cholesterol into the arteries, leading to plaque formation and atherosclerosis. Other steroids include the sex hormones testosterone, progesterone, and the estrogen family (estrone, estradiol, estratriol, etc.; Figure 12.30). images Figure 12.30 Some Common Steroids Prostaglandins Prostaglandins are powerful, but short-lived, hormones in mammalian systems that were first isolated from seminal fluid. The name prostaglandins is derived from “prostate gland.” Prostaglandins are synthesized in vivo from an unsaturated fatty acid called arachidonic acid. The identifying structural feature of a prostaglandin is a five-membered ring with a seven-carbon side chain, R7 (often ending in a carboxylic acid group) adjacent to an eight-carbon chain, R8. images Figure 12.31 shows some common prostaglandins. The letters PG stand for prostaglandin. The next letter indicates the functional groups in the ring. Sorry, there is no system to the letters. The number that follows indicates the number of double bonds in the side chains. In PGF2a, the alpha indicates the hydroxyl group on the lower side chain is pointed down (just as with the anomeric hydroxyl group in sugars). images Figure 12.31 The Prostaglandins images METABOLISM OF CARBOHYDRATES AND FATTY ACIDS Although carbohydrates and lipids play other roles in the body, one of our principal aims in eating fat and sugar is for the energy content. We need to access the energy stored in the chemical bonds of these compounds in order to move our muscles, keep our hearts beating, synthesize proteins and nucleic acids, and so on. Carbohydrates and triglycerides are metabolized through a series of chemical reactions, many of which are oxidation reactions. These pathways convert food molecules into high-energy biomolecules. The main high-energy molecule is adenosine triphosphate, more commonly known as ATP (Figure 12.32). ATP is the compound that our bodies most easily use for the processes of staying alive. images Figure 12.32 Adenosine Triphosphate However, there are a number of other high-energy molecules that are produced in the metabolism of carbohydrates and fats. The first one we’ll consider is acetyl coenzyme A (acetyl CoA). The structure of acetyl CoA is given in Figure 12.33. The acetyl portion of the molecule is shown in blue, and, although this is a bit of an oversimplification, you can think of this acetyl group as being derived from acetic acid. The carbons in the acetyl group are derived by breaking the carbon–carbon bonds in fatty acids and glucose into two-carbon units. images Figure 12.33 Acetyl Coenzyme A The acetyl portion is bonded to coenzyme A through a thioester functional group. In organic chemistry, “thio” means sulfur. So, a thioester is an ester in which one of the oxygen atoms has been replaced by a sulfur atom (see Figure 12.34). Because the carbon–sulfur bond is not as strong as the carbon–oxygen bond in a regular ester, acetyl CoA readily releases the acetyl group to other organic molecules. So, the role of coenzyme A is to shuttle the carbons from metabolism of glucose and fatty acids into the Krebs Cycle. Several reactions in metabolism are oxidation–reduction (or redox) reactions. Two of the principal redox carriers are nicotinamide adenine dinucleotide (NAD+) and coenzyme Q. Remember that we live in an oxidizing world, so species that are in the reduced form are frequently high-energy compounds that react exothermically with oxygen. Also recall that organic molecules are reduced by adding bonds to hydrogen. images Figure 12.34 Formation of a Thioester Figure 12.35 shows the reduction reaction of NAD+ into the reduced form, NADH. The added hydrogen on NADH is shown in blue. NADH is the energized form that can feed into the electron transport chain to synthesize ATP. images Figure 12.35 Nicotinamide Adenine Dinucleotide Figure 12.36 shows the reduction reaction of coenzyme Q into the reduced form, QH2. The added hydrogens are shown in blue. QH2 is the energized form that can feed into the electron transport chain to synthesize ATP. images Figure 12.36 Coenzyme Q Figure 12.37 gives the big picture for the metabolism of carbohydrates and triglycerides. images Figure 12.37 Overview of Metabolism Carbohydrates are generally converted into glucose, and glucose feeds into the glycolysis pathway. The six carbons in glucose are broken down into two three-carbon molecules of pyruvic acid, along with two molecules each of ATP and NADH for each glucose molecule metabolized. Glycolysis is shown in Figure 12.38. images Figure 12.38 Glycolysis Under anaerobic conditions, the pyruvic acid is reduced to lactic acid, which consumes the NADH produced (see Figure 12.39). Thus, anaerobic metabolism is highly inefficient because the more energetically valuable of the two high-energy products (NADH) is consumed. images Figure 12.39 Reduction of Pyruvic Acid Into Lactic Acid Under aerobic conditions, the pyruvic acid is converted into acetyl CoA. This pathway also provides an NADH, along with carbon dioxide, as shown in Figure 12.40. images Figure 12.40 Formation of Acetyl Coenzyme A Fatty acids are cleaved from triglycerides and metabolized through beta oxidation. This process is shown in Figure 12.41. Beta oxidation clips the fatty acids into two-carbon fragments. The two-carbon fragments emerge from beta oxidation as acetyl CoA. Each acetyl CoA molecule is accompanied by the production of an NADH and a QH2. Of course, when the chain is finally cut down to just two carbons, they are as an acetyl CoA. Since there are no carbon–carbon bonds to oxidatively cleave, no NADH or QH2 are produced. images Figure 12.41 Beta Oxidation of Fatty Acids The acetyl CoA molecules feed the Krebs Cycle, which is also known as the citric acid cycle or the tricarboxylic acid (TCA) cycle. Thus, one molecule of glucose can drive two rounds of the Krebs Cycle, whereas one molecule of stearic acid can drive nine rounds. The Krebs Cycle is the principal aerobic energy-producing pathway. Each turn of the Krebs Cycle affords one ATP5 molecule, three NADH molecules, and one QH2 molecule. Most of the energy produced directly from the Krebs Cycle is in NADH and QH2, both of which require oxygen to convert their stored energy into ATP. All of the reduced coenzymes, NADH and QH2, feed into the electron transport chain, and this is where the real energy payoff occurs. Through a series of oxidation–reduction reactions, where oxygen gas is the final oxidant, the energy stored in the reduced coenzymes drives the endothermic synthesis of ATP. On average, each NADH affords 2.5 ATP, and each QH2 furnishes 1.5 ATP. Thus, each acetyl Co A is worth 10 ATP. Table 12.2 summarizes the high-energy compounds derived from the metabolism of glucose and stearic acid. As you can see, fats offer much more energy than carbohydrates. Table 12.2 NET ATP FROM GLUCOSE AND STEARIC ACID images images PROTEINS AND AMINO ACIDS Proteins are one of the most remarkable of the biomolecules. Proteins serve many roles in living systems, from transport molecules, such as hemoglobin, to structural and locomotion tissues, to enzymes that are necessary to catalyze virtually every chemical process that living organisms carry out. Proteins are polymers of relatively simple organic compounds called amino acids joined together by peptide bonds. These “polypeptide chains” may contain just a few amino acids or more than 1,000 amino acids. When two amino acids are joined together, the protein is a dipeptide. When three amino acids are joined together, the protein is a tripeptide (etc.). When many amino acids are joined together, the protein is a polypeptide. So, while there are only about 20 common amino acids, there are nearly an infinite number of proteins. So, let’s take a closer look at amino acids and how they combine to give proteins. Amino Acids Amino acids contain two organic functional groups: an amine group and a carboxylic acid group (also known as a carboxyl group), as shown in Figure 12.42. These compounds are sometimes called alpha amino acids because the amine functional group is located on the first carbon out from the main functional group (the carboxylic acid). Each amino acid has a unique side chain that gives the amino acid its characteristic physical and chemical properties. The combined influences of all of the amino acid side chains confer both structure and function upon the protein. images Figure 12.42 Generic Amino Acid Side Chains The identity of an amino acid is determined by the side chain. It is easier to learn the side chains as organic groups (which is what they are). Each amino acid has a one-letter and a three-letter abbreviation. Although the three-letter abbreviations are more intuitive, most biochemists now use the one-letter abbreviations. Figure 12.43 gives the names, structures, and abbreviations of the amino acids, grouped according to the main functional group in the side chain. Figure 12.44 groups the amino acids according to their relative polarities. The least polar of the side chains are the hydrocarbon groups. The polar side chains include hydrogen-bonding functional groups such as alcohols and amides. Remember, hydrogen bonds are possible when a hydrogen atom is directly bonded to an oxygen atom or a nitrogen atom. The acidic and basic side chains are the most polar groups because they are largely in their ionized form (conjugate acid or conjugate base) at physiological pH. Stereochemistry of Amino Acids Naturally occurring amino acids belong to the L-family. That is, when the amino acid is drawn as a Fischer projection, with the carboxyl group at the top and the side chain at the bottom, the amino group is on the left, as shown in Figure 12.45. Since all amino acids (except glycine) are chiral, proteins are also chiral. Thus, the inherent handedness of proteins enables proteins to differentiate between two enantiomeric isomers. Recall that enantiomers have identical chemical and physical properties, except for how they interact with polarized light and other chiral species. For example, this is why we can digest D-sugars but not L-sugars. Acid–Base Properties of Amino Acids For the sake of clarity, we have been drawing amino acids incorrectly, and now it is time to recognize this error. Amino acids have both an acidic functional group and a basic functional group. Remember that acids donate hydrogen ions and bases accept hydrogen ions. The basic amino group takes a proton from the acidic carboxyl group. This intramolecular acid–base reaction results in formation of a zwitterion. A zwitterion is a species that is electrically neutral but has separated positive and negative ionic charges (see Figure 12.46). The word “zwitterion” comes from zwei, the German word for two. images Figure 12.43 Amino Acids and Their Abbreviations The carboxylate-ion-end of the zwitterion is the conjugate base of a weak acid and the ammonium-ion-end of the zwitterion is the conjugate acid of a weak base. Thus, the zwitterion is a buffer, and solutions of amino acids (and proteins) resist changes in pH. Zwitterions are an amphiprotic species and can behave as either an acid or a base. For example, if a strong acid, such as HCl, is added to a solution of an amino acid, the carboxylate-ion-end of the zwitterion accepts the proton from the stronger acid, and the zwitterion is converted into a cationic species. For convenience, let’s represent the zwitterionic form, which has one H+ to donate, as HA. The cationic form, which has two H+ ions to donate and has a net positive charge, is represented as H2A+, as can be seen in Figure 12.47. images Figure 12.44 Amino Acids Grouped by Polarity images Figure 12.45 L-Amino Acid images Figure 12.46 Formation of a Zwitterion images Figure 12.47 Formation of the Cationic Form of an Amino Acid The zwitterion can also behave as an acid and donate a hydrogen ion from the ammonium group. When the ammonium-ion-end of the zwitterion surrenders an H+ ion, the zwitterion is converted into an anionic form, A−, as can be seen in Figure 12.48. images Figure 12.48 Formation of the Anionic Form of an Amino Acid Thus, the net electrical charge on an amino acid is a function of pH, and this has both critical and useful implications. At very low pH, an amino acid is primarily in its fully protonated form (H2A+), and the net charge on an amino acid is positive. As pH increases, the cationic form is gradually converted to the zwitterionic form (HA), and the net charge approaches zero. As we continue to increase the pH to strongly basic conditions, the ammonium group surrenders the second proton, converting the amino acid into its fully deprotonated form (A−), and the net charge on an amino acid is negative. images An alpha plot is a convenient way to visualize the composition of an amino acid solution. Recall that alpha represents the percentage of each component in a chemical system. Let’s consider the alpha plot of glycine shown in Figure 12.49. In strongly acidic solutions (pH < 1), nearly 100% of the glycine molecules are present as the cationic form (H2A+). As we increase the pH, the concentration of the cation decreases and the concentration of the zwitterion increases. Notice that at α = 50%, the concentration of the weak acid (H2A+) is equal to the concentration of its conjugate base (HA). Since H2A+ is a weak acid and HA is its conjugate base, we have a buffer system. Recall that when the concentrations of the weak acid and its conjugate base are equal, the pH of the buffer is equal to the pKa of the weak acid. So, we see the pKa for H2A+ is equal to 2.3. images Figure 12.49 Alpha Plot for Glycine As we continue to increase pH, the zwitterion concentration reaches a maximum value at pH 6.0. Above this pH, the zwitterion is gradually converted into the anionic form (A−). Once again, we have a buffer system composed of a weak acid (HA) and its conjugate base (A−). The point where the alpha values for these two species equal 50% corresponds to a pH of 9.6, which is the pKa for the zwitterion. The Isoelectric Point The isoelectric point (pI) or isoelectric pH is the pH where the net charge on the amino acid is zero. At pI, the zwitterion is the dominant species, with an alpha value very close to 100%. The tiny equilibrium amounts of the cationic form and the anionic form are equal, so their opposite charges cancel each other out. The net charge on a collection of amino acid molecules at a pH less than pI is positive. The net charge on a collection of amino acid molecules at a pH greater than pI is negative. The pI is equal to the average of the two pKa values for the amino acid. For example, for a generic amino acid (HA), we can write two ionization equilibria and the corresponding equilibrium constant expressions. images If we add these two equilibrium equations together, we have: images Notice the equilibrium constant for these combined reactions equals the product of the individual equilibrium constant expressions, and the [HA] terms cancel out. images If we solve this expression for the hydrogen ion concentration, we have: images Now let’s specify that the hydrogen ion concentration is at the pI. Thus, [H2A+] = [A−], and our expression simplifies to: images Now, let’s take the negative logarithm of both sides of the equation: images Recalling that a log of a power is equal to the exponent times the log of the base, and the log of a product is equal to the sum of the logs, we can simplify the equation to: images Of course, the negative log of a quantity is the p-function, so we have: images Solving for pI, we have: images So, for glycine, if pKa1 = 2.3 and pKa2 = 9.6, what is pI for glycine? images So, at a pH of 6.0, the net charge on glycine is zero. At a pH less than 6.0, the average charge on the collection of glycine molecules is positive, and as the pH decreases, the average charge on the collection of glycine molecules approaches a maximum value of +1. At a pH greater than 6.0, the average charge on the collection of glycine molecules is negative, and as the pH increases, the charge approaches a maximum value of −1. Electrophoresis Electrophoresis is arguably the most important analytical tool in a biochemist’s repertoire. Electrophoresis uses an electric field to separate amino acids (or proteins or nucleic acids) on the basis of their electrical charge and molecular weight. When electrophoresis is applied to nucleic acid samples, it is commonly called DNA fingerprinting. The sample is placed on a solid support. The solid support looks and feels like Jello. Agarose is often used for DNA and polyacrylamide is often used for proteins. The gel is immersed in a buffer solution. The role of the buffer is not only to control the acid–base form of the amino acids (or whatever) present, but also to serve as an electrolyte (electrical conductor). A positive electrode is placed at one end of the gel and a negative electrode is placed at the other end. If the species has a charge, it will migrate toward the oppositely charged electrode. Species with a greater net charge move farther on the gel. So, the closer the buffer pH is to the pI of the sample, the less it moves. Smaller molecules with the same charge migrate faster than larger molecules, in accordance with Newton’s laws. The Peptide Bond A protein is a polypeptide chain consisting of amino acids joined by peptide bonds. Actually, though, a peptide bond is an amide bond formed between the amino group of one amino acid and the carboxyl group of another amino acid. For example, the reaction in Figure 12.50 shows formation of a dipeptide from two amino acids. images Figure 12.50 Formation of a Peptide Bond Notice that there is a direction in a polypeptide chain. One end of the chain has a free amino group, which is called the N-terminus. The other end of the chain has a free carboxyl group, and this is called the C-terminus. Figure 12.51 shows the structure of a tripeptide chain consisting of alanine, valine, and phenylalanine. Alanine is the N-terminal amino acid and phenylalanine is the C-terminal amino acid. images Figure 12.51 N-Terminal and C-Terminal Amino Acids Drawing the complete structure of the polypeptide chain is very time consuming, so biochemists typically give the abbreviations of the amino acids. So, the previous tripeptide can be expressed using either the three-letter or one-letter abbreviations: Ala-Val-Phe or A-V-F. When they are written this way, the N-terminal amino acid is always on the left. Primary Structure of Proteins. Video 12.1 The primary structure of a protein is the sequence of amino acids in the peptide chain. The primary structure is immensely important, because it is the sequence of amino acids that determines the higher levels of protein structure and, consequently, the function of the protein. Small changes in the primary structure can cause a protein to be completely nonfunctional. For example, sickle cell anemia is caused by the substitution of a single amino acid in the hemoglobin chain. Secondary Structure of Proteins The secondary structure of a protein is how the polypeptide chain is “twisted.” There are two common types of secondary structure: the alpha helix and the beta pleated sheet. In an alpha helix, the polypeptide chain is twisted into a coil, as illustrated in Figure 12.52. The “alpha” means the coil twists in a clockwise direction. The black spheres represent carbon atoms, the red spheres represent oxygen atoms, and the blue spheres represent nitrogen atoms. Hydrogen atoms are yellow. For the sake of clarity, only hydrogen atoms bonded to the amide nitrogen atoms are shown. The dashed lines represent hydrogen bonding between the hydrogen atoms on the nitrogen and carbonyl oxygen. images Figure 12.52 Alpha Helix Structure The beta pleated sheet, or simply beta sheet, structure is illustrated in Figure 12.53. The carbon backbone in the beta sheet is fully extended, and adjacent chains are held together by a large number of hydrogen bonds. images Figure 12.53 Beta Pleated Sheet Structure Tertiary Structure of Proteins The tertiary structure of a protein refers to how the alpha helices and beta sheet portions of a polypeptide chain are folded into a compact or globular structure. Two-dimensional representations of the three-dimensional tertiary structures of proteins are, well, pretty two-dimensional. If you want to better understand tertiary structure, you can view interactive, three-dimensional models of a large variety of proteins at the RCSB (Research Collaboratory for Structural Bioinformatics) Protein Data Base at http://www.rcsb.org. In addition to hydrogen bonding, tertiary structure is maintained by London forces and, sometimes, disulfide bridges. London forces act between nonpolar side chains that fold into the protein’s interior, away from the polar water environment. Disulfide bridges occur between different cysteine residues in the chain, as shown in Figure 12.54. The functional group in the cysteine chain is a sulfhydryl or thiol group. It is simply the sulfur analog of an alcohol. However, thiol groups are easily oxidized into disulfide groups that bridge two portions of the peptide chains, or between two different peptide chains. images Figure 12.54 Formation of a Disulfide Bridge By the way, this is the chemistry of a permanent hair wave. Hair is a protein rich in sulfur and has many disulfide bridges. First, hair is wrapped around a template, such as a curler. Then a mild reducing agent is applied to reduce some of the disulfide bridges present in hair. The physical stress of stretching the hair around a curler causes the polypeptide chains in hair to shift slightly with respect to each other. Finally, a mild oxidizing agent is applied, which creates new disulfide bridges that hold the hair in its deformed conformation. The Folding Problem The primary structure of the polypeptide chain determines the higher levels of structure. All proteins have a primary structure. Most proteins have a secondary structure, and compact globular proteins have a tertiary structure. Some proteins, such as hemoglobin, even have a quaternary structure, which is the association of globular proteins through noncovalent bonding interactions (e.g., hydrogen bonding) We can make some generalizations about how proteins fold. For example, it is a stabilizing feature to get hydrogen-bonding portions of the chain in close proximity. Proteins typically fold with nonpolar side chains on the interior of the protein, away from water, and with polar side chains on the outside of the protein, where they can interact with water molecules. In spite of these (gross) generalizations, the problem of how and why polypeptide chains fold into functional proteins remains one of the fundamental unsolved problems in physical biochemistry. Denaturing Proteins. Video 12.2 In order to be functional, globular proteins must retain their higher levels of structure. If something disrupts the higher levels of a protein’s structure, the protein is denatured and usually comes crashing out of a solution. An egg white is largely a solution of a protein called albumin. When you cook an egg, the heat denatures the albumin, and the denatured protein comes out of a solution to form the cooked white of the egg. In addition to high temperatures, heavy metal ions, such as Ag+ and Hg2+, and changes in pH can cause a protein to denature. Enzymes All living organisms are chemical factories, and virtually every chemical reaction that occurs in a living system is catalyzed by special proteins called enzymes. All enzymes are globular proteins. Folding the peptide chains into a compact structure creates a chiral pocket. This is called the active site of the enzyme. The extraordinary specificity that enzymes show for their given substrate molecules is because the active site exactly matches the dimension and shape of the molecules upon which the enzyme acts. One reason enzymes speed reaction rates is that enzymes capture reacting molecules and hold them in place next to each other. Furthermore, key amino acid side chains are located in the active site of each enzyme. For example, if a reaction is catalyzed by acid, then an acidic side chain will be located in the active site, exactly where it is needed to catalyze the reaction. images NUCLEIC ACIDS As we said earlier, nucleic acids are the architects and construction contractors for synthesizing proteins. There are two kinds of nucleic acids. DNA is the blueprint for synthesis of proteins. RNA is the construction contractor. Messenger RNA (m-RNA) reads the instructions for synthesis of a protein encoded on a strand of DNA and carries those instructions to the worksite, where transfer RNA (t-RNA) brings the amino acids in for incorporation into the polypeptide chain. Now, let’s take a closer look at the structures of DNA and RNA. DNA DNA is a biopolymer of phosphate sugars. Additionally, each phosphate sugar carries a nitrogenous base. The bases pair through hydrogen bonding, establishing a chemical basis for the genetic code. Now, let’s break down these components, so we can understand them. 2-Deoxyribose 2-Deoxyribose is an aldopentose that is the structural sugar in DNA. This sugar is called “deoxy” because it does not have a hydroxyl group on carbon 2. Deoxyribose cyclizes into a furanose (five membered) ring system. The structures of D-2-deoxyribose and β-D-2-deoxyribofuranose are given in Figure 12.55. images Figure 12.55 Deoxyribose Nucleosides: Adding the Nitrogenous Bases When we add a nitrogenous base to the sugar, we get a nucleoside, which is sometimes called a nucleoside base. DNA uses four bases, which fall into two categories: purines and pyrimidines. The four DNA bases are adenine, thymine, guanine, and cytosine. Adenine and guanine are purines because they are derivatives of the heteroaromatic compound purine. Thymine and cytosine are pyrimidines, because they are derivatives of the heteroaromatic compound pyrimidine. The structures of these compounds are shown in Figure 12.56. images Figure 12.56 The DNA Nitrogenous Bases Each base has a nitrogen atom capable of forming an acetal-like bond to the anomeric (or hemiacetal) carbon of deoxyribose. Recall that formation of an acetal from an alcohol and a hemiacetal involves elimination of water. We can envision that the water molecule is formed from the hydroxyl group of the hemiacetal and a hydrogen atom from the alcohol (or, in this case, the amine). Figure 12.57 illustrates this reaction for a purine base and for a pyrimidine base. So, there are four DNA nucleoside bases: deoxyadenosine, deoxythymidine, deoxycytidine, and deoxyguanosine. Usually, these bases are represented as dA, dT, dC, and dG, respectively. Often, the little d (which stands for deoxy) is omitted, and we simply use A, T, C, and G when describing the primary sequence of bases in DNA. Figure 12.58 gives the names and structures of these compounds. images Figure 12.57 Formation of DNA Nucleoside Bases images Figure 12.58 The DNA Nucleosides Nucleotides: Adding the Phosphate Group When we add a phosphate ester group to a nucleoside, we get a nucleotide. The phosphate ester group is (conceptually) added by the reaction of the hydroxyl group on carbon 5 (the one not in the ring) to phosphoric acid. In the example in Figure 12.59, deoxyadenosine forms a phosphate ester to give deoxyadenosine monophosphate. images Figure 12.59 Formation of a Nucleotide However, this reaction does not occur as written by simply mixing a nucleoside and phosphoric acid, and requires special reaction conditions. However, we are omitting those details for clarity. If you are interested, take a look in any modern biochemistry book. Phenomenologically, however, just as in other esterification reactions, a hydroxyl group from the acid combines with a hydrogen atom from the alcohol to give a water molecule. The remaining fragments join to afford the ester. When two acid molecules condense by elimination of a molecule of water, the product is called an acid anhydride, as can be seen in Figure 12.60. Acid anhydrides are always very reactive, or high-energy, compounds. When deoxyadenosine monophosphate forms an anhydride with phosphoric acid, we have deoxyadenosine diphosphate (dADP). Of course, if we add another phosphate group, we have deoxyadenosine triphosphate (dATP). images Figure 12.60 Formation of a Phosphate Anhydride Forming the DNA Strand The nucleosides are connected to the phosphate group by a phosphate ester functional group. Notice the phosphate group has additional OH groups, and those OH groups can be used to form additional phosphate ester bonds. Forming a new phosphate ester bond to the alcohol group on carbon 3 of another nucleotide strings the nucleotides into a strand of DNA. Notice there is a directionality to this chain illustrated in Figure 12.61. At the left end, the leading phosphate (shown in red) is bonded to carbon 3 of a deoxyribose unit. On the right end, the terminal phosphate (shown in green) is bonded to carbon 5 of the deoxyribose. The structure in Figure 12.61 shows the polymer in the 3′→5′ direction. Therefore, this strand of DNA could be represented as: (3′)C–T–A(5′) images Figure 12.61 A Short Strand of DNA This directionality is essential in transcription of DNA because it enables the transcription enzymes to read the genetic code in the proper direction. That is, C–T–A is not the same as A–T–C. Base Pairing The rigid rings in the bases hold hydrogen-bonding pieces in the exact location so that A always matches with T, and G always matches with C. The hydrogen bonds formed are illustrated in Figure 12.62. images Figure 12.62 Base Pairing Through Hydrogen Bonding Double-Stranded Helix In most cases, DNA found in the nucleus of a cell is a helical double-stranded structure. Figure 12.63 represents the double-stranded structure of a short section of DNA. The double strand is rather like a ladder. The sides of the ladder are formed by the phosphate sugar backbone. The rungs of the ladder are formed by the nitrogenous bases. The shape of the deoxyribose units forces the double strand into a helical shape (Figure 12.64). Carbon atoms are black, oxygen atoms are red, and nitrogen atoms are blue. The ladder appears to have been twisted around a flagpole. The deoxyribose units are chiral, and their chirality is evident in the overall structure of the helix, which is also chiral. You can run your right hand along the helix (and stay in the groove), but not your left hand. Since the helix twists to the right, it is called an alpha helix. images Figure 12.63 Model of Double-Stranded DNA images Figure 12.64 Helical Structure of DNA In forming a double helix, two complementary strands of DNA come together. That is, wherever there is an A in the first strand, there is a T in the second strand, and so forth. The double strand is held together by hydrogen bonding between the base pairs. Figure 12.65 illustrates this base pairing. Each strand of DNA has two nucleotides, both with a base sequence of T–A. The hydrogen bonds between the base pairs are represented by dotted lines. images Figure 12.65 A Short Section of Double-Stranded DNA Why the double strand? The integrity of DNA is of utmost importance, and the double strand provides a mechanism for ensuring that the base sequence in each DNA strand remains intact. If an incorrect base is accidentally incorporated into one of the strands, it won’t match its complement in the other strand, and repairs will be initiated to replace that base. RNA RNA has an identical structure to DNA, except for two features. The sugar backbone is composed of ribose, not deoxyribose, and RNA does not contain the base thymine. Instead, it uses the base uracil. Ribose Ribose is an aldopentose that is the structural sugar in RNA. Ribose cyclizes into a furanose (five-membered) ring system. The structures of D-ribose and β-D-ribofuranose are given in Figure 12.66. images Figure 12.66 Ribose RNA Nucleosides The four RNA bases are adenine, uracil, guanine, and cytosine. RNA does not use thymine. The structures of these compounds are shown in Figure 12.67. images Figure 12.67 The Ribonucleic Acid Nitrogenous Bases Base Pairing Just as with DNA, the bases have a geometry that ensures that A always matches with U and G always matches with C. The hydrogen bonds that ensure this pairing are illustrated in Figure 12.68. images Figure 12.68 Base Pairing Through Hydrogen Bonding If we attach the nitrogenous bases to a ribose, we have the RNA nucleosides. The four RNA nucleoside bases are adenosine, uridine, cytidine, and guanosine. Usually, these nitrogenous bases are represented as A, U, C, and G, respectively. Figure 12.69 gives the names and structures of these compounds. Addition of a phosphate group to carbon 5 of the ribose sugar affords the RNA nucleotide bases. images Figure 12.69 The Ribonucleic Acid Nucleosides Forming the RNA Strand Just as with DNA, phosphate esters link the RNA nucleotides into a strand of RNA. One role of the bases in the RNA strand is to match up to the bases in a sequence of DNA. For example, in Figure 12.70, the RNA strand reads: C − U − A images Figure 12.70 A Short Strand of Ribonucleic Acid This RNA strand would match DNA with the sequence: G − A − T m-RNA and t-RNA m-RNA is synthesized in the nucleus directly from DNA. Its job is to carry the instructions coded on the DNA out into the cytoplasm, where protein synthesis will occur. While m-RNA can adopt more complicated structures, we can think about m-RNA as a simple, straight chain of nucleotides. t-RNA is present in the cytoplasm. Each t-RNA carries a single amino acid. t-RNA is a much more complicated structure than m-RNA. Figure 12.71 shows a model of t-RNA. images Figure 12.71 Transfer Ribonucleic Acid The blue line represents a chain of RNA nucleotides; a sequence of three bases, known as the anticodon, is represented by the green shapes at the bottom of the structure. Each t-RNA has a specific amino acid attached to the 3′ terminal end. The anticodon determines which amino acid the t-RNA will pick up. Protein Synthesis Protein synthesis involves many steps, but the broad overview of the process begins with DNA. A section of DNA that contains enough information to make one protein is called a gene. The code is first transcribed from a strand of DNA into a strand of m-RNA. Then, the code now contained on the m-RNA strand is translated into a protein using t-RNA. The sequence of bases in DNA ultimately determines the sequence of amino acids in the peptide chain. Remember that the structure and function of a protein are determined by its primary structure, and the primary structure of a protein is determined by the primary structure (base sequence) in DNA. Each amino acid code consists of a three-base sequence. For example, the DNA sequence CGA codes for the amino acid alanine.6 This sequence in DNA codes for the m-RNA sequence GCU. A three-base pair in m-RNA that codes for an amino acid is called a codon. An anticodon is the three-base sequence in t-RNA that matches a codon in m-RNA. Transcription Transcription is the process of forming a complementary m-RNA strand from the DNA. This process occurs in the cell nucleus. To begin, an enzyme helps the DNA double helix to break apart and uncoil slightly. This allows RNA nucleotide bases to form complementary hydrogen bonds to the DNA bases. In essence, the m-RNA is reading the DNA code. For example, let’s imagine a short section of DNA with the following sequence: A − A − T − G − C − C − G − A − A First, an RNA base with a U matches up to the first base in the DNA strand (A). Remember that A always pairs with U, C always pairs with G, and T always pairs with A. Also, don’t forget that DNA has the T base and RNA has the U base. The RNA nucleotide is held in place by hydrogen bonding. Then a second RNA base (U) hydrogen-bonds to the second base on the DNA strand, and it is also held in place by hydrogen bonding. Then, an enzyme establishes a phosphate ester link between the two RNA nucleotides, forming an m-RNA strand containing two bases. This process is repeated until all nine RNA nucleotides are stitched together into an m-RNA strand. This is shown in Figure 12.72. So, the sequence in our m-RNA strand (and the complementary DNA strand) is illustrated in Figure 12.73. This nine-base strand of m-RNA contains three codons: UUC, GGC, and AUU, and calls for the amino acids phenylalanine, glycine, and isoleucine, in that order.7 Thus, the order of the bases in DNA dictates a particular sequence in the m-RNA strand. When the m-RNA strand is complete, it leaves the nucleus and heads for the ribosomes in the cytoplasm. images Figure 12.72 Transcription of DNA Into Messenger Ribonucleic Acid images Figure 12.73 Transcribing DNA Into Messenger Ribonucleic Acid Translation Translation is the process of pairing an amino-acid-bearing t-RNA to the m-RNA (see Figure 12.74). The three-base codon sequence on the m-RNA must match the three-base anticodon sequence on the t-RNA. If the anticodon matches the codon, the t-RNA, along with its amino acid, will be held in place on the m-RNA chain by hydrogen bonding. From our previous example, the first codon in the m-RNA is UUA. Only a t-RNA with the anticodon AAU will pair up to this codon. The t-RNA with this anticodon carries the amino acid isoleucine. Then the next t-RNA settles into place, and an enzyme establishes a peptide bond between the amino acids bound to the t-RNA. Forming the peptide bond requires the expenditure of an ATP molecule, so protein synthesis is energetically expensive. This is why we use our fat reserves, rather than muscle, when our energy expenditures exceed our food intake. Once the amino acid has been cleaved from the t-RNA, the t-RNA is released from the m-RNA chain and proceeds back out into the cytoplasm to pick up another amino acid. This process continues until the synthesis of the polypeptide chain is complete. images Figure 12.74 Translation of DNA Into Messenger Ribonucleic Acid SUMMARY Biomolecules are the molecules that comprise living systems. Biomolecules include carbohydrates, lipids, proteins and amino acids, and nucleic acids. Carbohydrates are polyalcohol aldehydes or ketones. Monosaccharides are not easily broken down into simpler sugars by the action of dilute aqueous acid. Polysaccharides are broken down into monosaccharides by dilute aqueous acid. Most carbohydrates are chiral, which means they are not superimposable on their own mirror image. Naturally occurring monosaccharides belong to the D family, which means the next-to-last OH group in the Fischer projection is pointed to the right. Monosaccharides form cyclic hemiacetals or hemiketals by the addition of one of the alcohol functional groups across the carbonyl double bond. The resulting cyclic hemiacetals/ketals contain five- or six-membered rings. Monosaccharides can combine by the condensation of an alcohol functional group of one monosaccharide with the hemiacetal functional group of a second. The resulting acetal functional group is known as a glycoside bond. Lipids are characterized by a physical property. Lipids are more soluble in organic solvents, such as ether, than in water. Saponifiable lipids are broken down into fatty acids by the action of hot aqueous base. Triglycerides are a common saponifiable lipid. Triglycerides are tri-esters of glycerin and three fatty acids. A fatty acid is a carboxylic acid having a carbon backbone containing 12 to 18 carbon atoms. Fatty acids are saturated if there are no carbon–carbon double bonds. Fatty acids having one or more carbon–carbon double bonds are termed unsaturated. Naturally occurring unsaturated fatty acids contain cis double bonds. Nonsaponifiable lipids include steroids and prostaglandins. Carbohydrates and fatty acids are the principal energy sources. Polysaccharides are broken down into glucose. Glycolysis converts this six-carbon sugar into a pair of three-carbon sugar-acids (lactic acid or pyruvic acid) plus some energy. Pyruvic acid is converted into acetyl coenzyme A, which feeds into the Krebs Cycle. Fatty acids are broken down acetyl coenzyme, which is also fed into the Krebs Cycle. The Krebs Cycle is the most efficient energy production pathway, giving some ATP but, more importantly, producing reduced coenzymes, such as NADH2. The electron transport chain uses NADH2 to make ATP. Amino acids contain two organic functional groups: a carboxylic acid and an amine functional group. Amino acids also contain a side chain group, which largely determines the physical and chemical properties of the amino acid. Side chains may be nonpolar hydrocarbon functional groups, polar alcohol or amide functional groups, or ionic acidic/basic functional groups. Nonpolar side chains interact by London forces, and are often located in the interior of a protein, away from the polar water solvent. Polar side chains interact by dipole–dipole interactions and/or hydrogen bonding. Ionic side chains interact by ion–ion and ion–dipole interactions. Amines are bases, so the amine functional group is converted into its positively charged conjugate acid at low pH. The carboxylic acid functional group is converted into its negatively charged conjugate base at high pH. At intermediate pH, an amino acid is electrically neutral. This pH is called the pI. Proteins are formed by condensing the amine functional group of one amino acid with the carboxylic acid functional group of another. The resulting amide functional group is called a peptide bond. The protein is sometimes called a polypeptide. The primary structure of a polypeptide chain is the sequence of the amino acids in the chain. The primary structure is ultimately responsible for all higher levels and structure and, therefore, the function of the protein. There are two common secondary structures for a polypeptide chain. The alpha helix has the chain coiled into a helix. The beta pleated sheet has the polypeptide chain fully extended. Both the alpha helix and the beta pleated sheet are maintained by hydrogen bonding that occurs between the hydrogen atom on an amide nitrogen with an oxygen in a carbonyl group. The tertiary structure of a polypeptide chain describes how the chain is folded into a compact, globular structure. The tertiary structure is maintained by hydrogen bonding and London forces. Addition of an organic solvent, changing the pH, or adding a heavy metal ion disrupts these stabilizing forces and causes the protein to lose its tertiary (and secondary) structure. This is called denaturing. Denatured proteins are inactive and often precipitate out of solution. Nucleic acids are polymers consisting of five-carbon sugar molecules (ribose in RNA or deoxyribose in DNA) lined together by phosphate groups. Each sugar molecule also carries a nitrogenous base. A nucleoside is a sugar (ribose or deoxyribose) bonded to a nitrogen base. There are four nucleoside bases in DNA: adenosine (A), guanosine (G), thymidine (T), and cytidine (C). In RNA, thymidine is replaced with uridine (U). Condensation of a phosphate group with the alcohol functional group of carbon 5 of the sugar in a nucleoside gives a phosphate ester called a nucleotide. The phosphate group can form more than one ester functional group. So, condensation of the phosphate in one nucleotide with the alcohol functional group on carbon three of a second nucleotide joins the two nucleotides into a dinucleotide. RNA and DNA are polymers that contain thousands of nucleotide bases, joined together by phosphate ester bridges. DNA consists of two strands of polynucleotide chains. The double strands are held together by base-pairing. Because of the molecular geometry, A fits with T to form two hydrogen bonds. Likewise, C and G fit together to form three hydrogen bonds. Base-pairing means the A in one strand of DNA will always pair with a T in the other strand. Likewise, C always pairs with G. The primary structure of DNA is the sequence of bases, and the sequence of bases forms the genetic code, and contains the information needed to synthesize proteins. There are two kinds of RNA: m-RNA and t-RNA. t-RNA is a polynucleotide chain that transcribes the genetic code from DNA. The structure of t-RNA is the same as DNA, except the sugar is ribose, not deoxyribose. Transcription of the genetic code is achieved through base-pairing. If the DNA has a C base, the corresponding t-RNA chain will have a G base. If the DNA has a G base, the corresponding RNA will have a C base. If the DNA has a T base, the RNA will have an A base. In RNA, T has been replaced with U, so if the DNA has an A base, the RNA will have a U base. So, transcription of the DNA sequence GATACA leads to synthesis of the m-RNA sequence CUAUGU. A codon is a three-base sequence on the m-RNA chain that codes for a specific amino acid. Translation of the genetic code is achieved by matching t-RNA molecules onto the m-RNA chain. t-RNA carries an amino acid and a three-base sequence called an anticodon. Base pairing ensures that the three-base sequence in a codon on the m-RNA chain will specifically match to a three-base sequence in the anticodon in a t-RNA molecule that carries a specific amino acid. As each sequential t-RNA fits its anticodon to the codons on the m-RNA, the amino acids carried by the t-RNA are fit together in specific sequence. Thus, the sequence of bases in DNA is translated and then transcribed into a sequence of amino acids in a polypeptide chain. REVIEW QUESTIONS FOR BIOCHEMISTRY 1.Which of the following objects are chiral: an ear, a glove, a bolt, a femur, a soda can (ignore the writing), a human body (ignore minor differences on the right and left sides and the internal anatomy)? 2.Alpha linolenic acid is an omega-3 unsaturated fatty acid. What does omega-3 mean? If linolenic acid has 18 carbon atoms and the positions of the double bonds are Δ9,12,15, what is the structure of alpha linolenic acid? 3.Draw the structure of α-D-ribofuranose. 4.As a polypetide chain is folding into a compact structure, where do you expect the side chains on amino acids such as valine and phenylalanine will wind up? Where will the side chains on amino acids such as serine wind up? 5.Wool and silk are both proteins. One is predominantly a beta pleated sheet and the other is predominately an alpha helix. Which is the alpha helix and which is the beta pleated sheet? 6.You doubtless learned in a nutrition course that fats have twice the energy content of carbohydrates. The molecular formula of glucose is C6H12O6. The molecular formula of stearic acid is C18H36O2. How many ATPs are produced per gram of glucose, and how many ATPs are produced per gram of stearic acid? 7.If the base sequence in a section of DNA is A–T–C, what is the base sequence in the complementary strand of DNA? What is the sequence of the m-RNA? What is the sequence of the t-RNA? 8.The order of amino acids in a peptide chain is the: a.Primary structure b.Molecular formula c.Codon code 9.Which are held together by peptide bonds? a.Nucleic acids b.Polysaccharides c.Proteins 10.The molecule that carries the genetic message from the nucleus to the ribosomes is: a.DNA b.m-RNA c.t-RNA 11.A polymer of β-glucose is: a.Starch b.Cellulose c.Amylose 12.Which of these biomolecules performs the function of catalyzing a biochemical reaction? a.Proteins b.Enzymes c.DNA 13.All naturally occurring amino acids belong to which optical family? a.L b.D c.Some are D and some are L. 14.Carbohydrates that are hydrolyzed into simpler carbohydrates by aqueous acid are called: a.Complex carbohydrates b.Polymers c.Polysaccharides 15.Sucrose is a disaccharide composed of: a.Two glucoses b.Maltose and lactose c.Glucose and fructose 16.The group of biomolecules characterized by their solubility in organic solvents are the: a.Lipids b.Carbohydrates c.Nucleic acids 17.A triglyceride is composed of glycerin and three: a.Terpenes b.Sugars c.Fatty acids 18.The pH at which the net charge on an amino acid is zero is called the: a.Isoelectric pH b.Zero charge pH c.Neutrality point 19.A protein is spotted onto a piece of filter paper wetted with a pH buffer lower than the pI of the protein. This paper is placed in a DC electric field. The protein will: a.Migrate toward the positive electrode b.Move toward the negative electrode c.Not move 20.Virtually all naturally occurring sugars are: a.L-Sugars b.D-Sugars c.Sweeter than glucose 21.Poly alpha glucose is more commonly known as: a.Starch b.Sucrose c.Cellulose 22.An unsaturated triglyceride has: a.A lower melting point b.Few double bonds c.A higher smoke point 23.Heating most globular proteins will cause them to lose their three-dimensional shape. This is called: a.Denaturing b.Coagulation c.Frying 24.Which nucleotide base is present in DNA but absent in RNA? a.Adenine b.Thymine c.Uracil 25.Select the true statement: a.t-RNA transfers the genetic code from the nucleus to the site of protein synthesis. b.The t-RNA chain base sequence is directly coded from DNA. c.The primary structure of RNA is determined by the DNA. 26.The DNA sequence GAT requires which anticodon sequence in t-RNA? a.CUA b.GAU c.GTU images 1 For the sake of simplicity, we admit to being somewhat cavalier in our use of the terms right-handed and left-handed. Interested readers are directed to any modern organic chemistry textbook. 2 This is not strictly true. There are some special (and rare) classes of molecules that are chiral because of restricted rotation around single or double bonds that impose a nonplanar and chiral conformation. Substituted allenes are the classic example of axially dissymmetric chiral molecules. 3 http://www.fda.gov/drugs/guidancecomplianceregulatoryinformation/guidances/ucm122883.htm 4 Starkey, R. (2000). SOS: A mnemonic for the stereochemistry of glucose. Journal of Chemical Education, 77, 734. 5 Actually, the product is guanosine triphosphate (GTP), but GTP is energetically equivalent to ATP. 6 For the sake of clarity, we are being somewhat cavalier about directions on the DNA and RNA strands. Please consult a biochemistry text if you wish to explore this topic in greater depth. 7 We know this is confusing. m-RNA is read 5′→3′, from right to left, as we have written the strand.