Molecular Structures: DNA and Importance

320 Chapter 7 | MOLECULAR STRUCTURES acids are hydrophobic, or “water-fearing”; they are held together by London forces and...

320 Chapter 7 | MOLECULAR STRUCTURES acids are hydrophobic, or “water-fearing”; they are held together by London forces and point away from the aqueous environments. The result is separation of the interior of a cell from the surrounding fluids by the lipid bilayer, a separation that allows control over which ions or molecules enter a cell and which chemical reactions can occur within the cell. In our bodies, noncovalent interactions bring molecules of metabolic products, drugs, hormones, and neurotransmitters (nervous system messengers) into contact with cellular receptors. The receptors are often proteins embedded in the cell membrane’s lipid bilayer. Hydrogen bonding, dipole-dipole forces, and London forces help to align the target molecule with its particular site on the receptor surface. Once a chemical mes- senger connects with its receptor, the messenger may enter the cell to initiate a chemical reaction, or a reaction may occur as a result of changes initiated by the receptor. 7-7 of Biomolecules: DNA and the Importance Molecular Structure Nowhere do the shape of a molecule and noncovalent forces play a more intriguing and important role than in the structure and function of deoxyribonucleic acid (DNA), the molecule that stores the genetic code. Whether you are male or female, have blue or Volker Steger/Science Source brown eyes, or have curly or straight hair depends on your genetic makeup. These and all your other physical traits are determined by the composition of the approximately 1 m of tightly coiled DNA that makes up the 23 double-stranded chromosomes in the nucleus of each of your cells. DNA. Solid DNA is precipitated from solution. 7-7a Nucleotides of DNA DNA is a polymer, a molecule composed of many small, repeating units bonded to- gether. Each repeating unit in DNA, called a nucleotide, has the three connected parts shown in Figure 7.24—one sugar unit, one phosphate group (phosphoric acid unit), and HOCH2 Base 1 O H H H H O H −O P O The deoxyribose units in the backbone chain are joined O Adenine unit– through phosphate diester a nitrogenous base Base 2 linkages. Phosphoric acid is CH2 O H3PO4, OPP(OH)3. NH2 Phosphoric H H acid unit H H HO Deoxyribose unit– N N phosphoric O a simple sugar O H HO P O N acid −O H O P O CH2 O N P O HO OH H H O Replacing two H atoms H H Base 3 with two CH3 groups gives OH H CH2 O a phosphate diester, H H OPP(OH)(OCH3)2. H H A nucleotide consists of a O H H 3C O phosphate (phosphoric acid phosphate unit), a sugar (deoxyribose in −O P O HO P O diester the case of DNA), and a H3C O nitrogen base such as adenine. O− Figure 7.24 Nucleotides and DNA. The phosphate groups and the deoxyribose sugar groups form the backbone of DNA. The genetic code is carried by the nitrogenous bases. Unless otherwise noted, all content on this page is © Cengage Learning. Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.  7-7 Biomolecules: DNA and the Importance of Molecular Structure 321 a cyclic nitrogen compound known as a nitrogen base. In DNA the sugar is always deoxyribose and the base is one of four bases—adenine (A), thymine (T), guanine (G), or cytosine (C). The bases are often referred to by their single-letter abbreviations. A DNA segment with nucleotides bonded together is shown in Figure 7.24. The phosphate units join nucleotides into a polynucleotide chain that has a backbone of alter- nating deoxyribose and phosphate units in a long strand with the various nitrogenous bases extending out from the sugar-phosphate backbone. The order of the nucleotides (and thus the particular sequence of bases) along the DNA strand carries the genetic code DOE/Science Source from one generation to the next. 7-7b The Double Helix: The Watson-Crick Model Francis H. C. Crick (right) and In the early 1950s, Erwin Chargaff measured the quantities of nitrogen bases in DNA James D. Watson. Working in the samples from a broad range of organisms. Based on his analyses, it was apparent that in Cavendish Laboratory at Cambridge, England, Watson and Crick built a scale any given organism, from a human genius to a bacterium, model of the double-helical structure, the base composition is the same in all cells of the organism and is characteristic based on X-ray data. Knowing distances and angles between atoms, they of that organism. compared the task to working on a the quantities of adenine and thymine are equal, as are the quantities of guanine three-dimensional jigsaw puzzle. Watson, and cytosine. Crick, and Maurice Wilkins received the 1962 Nobel Prize in Physiology or the sum of the quantities of adenine plus guanine equals the sum of the quantities Medicine for their work relating to the of cytosine plus thymine. structure of DNA. Two deoxyribose–phosphate The backbones (red) Complementary bases (blue) backbones are joined to twist together in a are connected by hydrogen bases lying in the center. double helix. bonds (dashed line). Figure 7.25 Double-stranded DNA. The illustration shows the deoxyribose-phosphate backbone of each strand as phosphate groups (orange and red) linking five-membered rings of deoxyribose joined to bases. The complementary bases (shown in blue) are connected by hydrogen bonds: two between adenine and thymine, and three for guanine and cytosine. Unless otherwise noted, all content on this page is © Cengage Learning. Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it. 322 Chapter 7 | MOLECULAR STRUCTURES Rosalind Franklin This information implied that the bases occurred in pairs: adenine with thymine and 1920–1958 guanine with cytosine. Using X-ray crystallography data gathered by Rosalind Franklin and Maurice Wilkins on the relative positions of atoms in DNA, plus the concept of A-T and G-C base pairs, the American biologist James D. Watson and the British physicist Francis H. C. Crick proposed a double helix structure for DNA in 1953. In the three-dimensional Watson-Crick structure, two polynucleotide DNA strands wind around each other to form a double helix. Remarkable insight into how hydrogen bonding could stabilize DNA ultimately led Watson and Crick to propose the double helix structure. Hydrogen bonds form between specific base pairs lying opposite each other in the two polynucleotide strands. Adenine is hydrogen-bonded to thymine and Science Source guanine is hydrogen-bonded to cytosine to form complementary base pairs; that is, each base in one strand hydrogen bonds to its complementary base in the other strand (Figure 7.25). The result is that the base pairs (A on one strand with T on the other strand, R osalind Franklin received her or C with G) are stacked one above the other in the interior of the double helix (blue in degrees from Cambridge Univer- Figure 7.25). sity. Her most famous work was Two hydrogen bonds occur between every adenine and thymine pair; three occur be- the first X-ray photographs of DNA, done in collaboration with tween each guanine and cytosine pair. These hydrogen bonds hold the double helix to- Maurice Wilkins at King’s College gether. Note in Figure 7.26 the similar structures of thymine and cytosine, and of adenine in London, showing two forms of and guanine. If adenine and guanine try to pair, there is insufficient space between the DNA, one of them a helix. By in- strands to accommodate the bulky pair; thymine and cytosine are too small to pair and to terpreting these X‑ray data, James align properly. Watson and Francis Crick derived their now-famous double helix Conceptual Exercise 7.8 model of DNA for which they, along with Wilkins, received the Hydrogen Bonding and DNA 1962 Nobel Prize in Physiology or Only one hydrogen bond is possible between G and T or between C and A. Use the Medicine. Rosalind Franklin’s un- structural formulas for these compounds to indicate where such hydrogen bonding can timely death of ovarian cancer at occur in these base pairs (see Figure 7.26). the age of 37 resulted in her not sharing that award. Nobel Prizes are not awarded posthumously. 7-7c The Genetic Code and DNA Replication In the historic article in a scientific journal that described their revolutionary findings, Watson, J. D., and Crick, ­Watson and Crick wrote, “It has not escaped our notice that the specific pairing we have F. H. C., Nature, Vol. 171, 1953, postulated immediately suggests a possible copying mechanism for the genetic material.” p. 737. This bit of typical British understatement belies the enormous impact that deciphering DNA’s structure had on establishing the molecular basis of heredity. It was now clear that the DNA sequence of base pairs in the nucleus of a cell represents a genetic code that controls the inherited characteristics of the next generation, as well as most of the life The total sequence of base processes of an organism. pairs in a plant or animal cell is In humans, the double-stranded DNA forms 46 chromosomes (23 chromosome called its genome. pairs). The gene that accounts for a particular hereditary trait is usually located in the ne bo ne To k bo ac ck ba To b ba To ck ba To bo c ne kb on thymine adenine cytosine guanine e Figure 7.26 Hydrogen bonding (...) between complementary base pairs, T-A and C-G, in DNA. Unless otherwise noted, all content on this page is © Cengage Learning. Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.  7-7 Biomolecules: DNA and the Importance of Molecular Structure 323 A C T G G G T T C A Old DNA G C T A strand C A A C G A A G C G T T A T A C New DNA G A T strand T C G G G A C T A A New DNA G C T G Original strands T A DNA molecule C New DNA C A T A strand A C G T C T Old DNA strand Figure 7.27 DNA replication. When the original DNA helix (orange) unwinds, each half is a template on which nucleotides from the cell environment assemble to produce a complementary strand (green). Each new double strand is an exact replica of the original. same position on the same chromosome. Each gene is a unique sequence of nitrogen bases that codes for the synthesis of a single protein within the body. The gene can be “read” by chemical processes involving RNA (ribonucleic acid, which has a structure closely related to DNA’s structure) and used to control synthesis of a protein molecule. The protein then goes on to play its role in the growth and functioning of the individual. (Proteins are discussed in Section 10-7d.) Each organism (except viruses) begins life as a single cell. The double-stranded DNA in that cell consists of a single strand from each parent. During regular cell divi- sion, both DNA strands are accurately copied, with a remarkably low incidence of error. The copying of a DNA molecule, called replication, takes place as enzymes aid in break- ing hydrogen bonds between strands, unzipping the DNA helix. New nucleotides are sequentially brought into the proper places on each of two new strands so that they pair with bases on the old strands. Thus, each strand of the original DNA serves as a template from which a complementary strand is produced (Figure 7.27). The process is termed semiconservative because in each of two new cells, each chromosome consists of one DNA strand from the parent cell and one newly made strand. Estimation Base Pairs and DNA Human DNA contains about three billion base pairs, which are Thus, there are about 6 × 107 base pairs in genes/DNA. an average distance of 0.34 nm apart in the DNA molecule. Using this information and the fact that DNA contains about Only about 2% of this DNA consists of unique genes. The num- 2 × 104 genes, there are roughly 3 × 103 base pairs/gene. ber of genes is estimated to be 2 × 104. 6 × 10 7 base pairs in genes 1 DNA mollecule 3 × 10 3 base pairs (a) Calculate the average number of base pairs per gene. × ≅ DNA molecule 2 × 10 genes 4 gene (b) Calculate approximately how long (m) a DNA molecule is. (b) To approximate how many meters long a DNA molecule is, (a) We begin by calculating the average number of base we use the information that the distance between base pairs pairs/gene, starting with approximately 3 × 109 base pairs, in DNA is 0.34 nm and 1 m = 109 nm. Therefore, of which there are 2 base pairs in genes per 100 base pairs. We get 3 × 10 9 base pairs 0.34 nm 1m 1m × × ≅ DNA molecule base pair 10 9 nm DNA molecule 3 × 10 9 base pairs 2 base pairs in gennes × This distance, approximately 1 m (about three feet), would be DNA molecule 100 base pairs much too large to fit into a cell. Therefore, the DNA molecule 6 × 10 7 base pairs in genes must be tightly coiled, which it is. = DNA molecule Unless otherwise noted, all content on this page is © Cengage Learning. Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it. 324 Chapter 7 | MOLECULAR STRUCTURES Conceptual Exercise 7.9 Replication and Base Pairing in DNA How easily would the base pairs in DNA unpair during replication if they were linked by covalent bonds? How is it that the helix unzips so readily? Summary Problem Part I Write the Lewis structures and give the electron-region geometry, molecular geometry, and bond angles, and the hybridization of the central atom of these polyatomic ions and molecules. (a) BrF+ + − 2     (b) OCCl2   (c) CH3     (d) SeCS    (e) CH3 Part II Aspartame is a commonly used artificial sweetener (NutraSweet®) that was discovered acciden- tally by a chemist in the laboratory carelessly licking his fingers after synthesizing a new com- pound (aspartame). The sweetener’s popularity stems from the fact that aspartame tastes over 100 times sweeter than sugar. Aspartame has this structural formula. H O H O H H N C C N C C O C H H H C H H H C H H O C O H (a) Write the molecular formula of aspartame. (b) Identify three atoms that have triangular planar molecular geometry. (c) Identify three atoms that have tetrahedral molecular geometry. (d) Identify two atoms that have bent (angular) molecular geometry. (e) Identify the hybridization of each nitrogen atom. (f) Identify the hybridization of carbon in the CH2 groups. (g) Identify the hybridization of the carbon atom in the CPO group. (h) Identify the hybridization of the oxygen atom to which a methyl (OCH3) group is attached. (i) Label each of the sigma and pi bonds involving carbon and those involving nitrogen. Part III The structural formula for the open-chain form of glucose is O H OH H H H C C C C C C OH H OH H OH OH H Glucose dissolves readily in water. Use molecular structure principles to explain why glucose is so water-soluble. Unless otherwise noted, all content on this page is © Cengage Learning. Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.  10-7 Biopolymers: Polysaccharides and Proteins 463 including California, which, since 1995, requires all HDPE packaging to contain 25% re- cycled HDPE. A significant challenge lies ahead in finding economically viable methods to recycle plastics (and metals) from the rapidly increasing and massive numbers of ob- solete personal computers and mobile electronic devices. The U. S. EPA estimates that 225,000 tons of personal computers and 17,200 tons of mobile digital devices were dis- carded in 2010; about 40% of personal computers and 11% of mobile devices were recy- cled. To combat having such electronic waste (“e waste”) end up in landfills or being incinerated, stricter laws are being put into place at the state and local levels regarding disposal and recycling of such waste. 10-7 Biopolymers: and Proteins Polysaccharides Biopolymers—naturally occurring polymers—are an integral part of living things. Many advances in creating and understanding synthetic polymers have come from studying biopolymers. Cellulose and starch, made in plants by condensation polymerization reac- tions, resemble synthetic polymers in that the monomer molecules—glucose—are all alike. On the other hand, proteins, which are made by both plants and animals, differ from synthetic polymers because they include many different monomers. Also, the oc- currences of the different monomers along the protein polymer chain are anything but regular. As a result, proteins are extremely complex condensation copolymers. 10-7a Monosaccharides to Polysaccharides Nature makes an abundance of compounds with the general formula ­Cx(H2O)y, in which x and y are whole numbers, such as in glucose, C6H12O6, where x = 6, y = 6. These com- pounds are variously known as sugars, carbohydrates, and mono-, di-, or polysaccharides (from the Latin saccharum, “sugar”—because they taste sweet). The simplest carbohy- drates, such as glucose, are monosaccharides, also called simple sugars, because they contain only a single saccharide molecule. Disaccharides consist of two monosaccharide units joined together, such as sucrose (table sugar, glucose and fructose linked) or maltose (two glucose units linked). Polysaccharides are polymers containing many monosaccha- ride units, up to several thousand. This chart summarizes carbohydrate terminology. Carbohydrates Monosaccharides Disaccharides Polysaccharides One sugar unit Two sugar units Many sugar units per molecule per molecule per molecule Examples: Examples: Examples: glucose, sucrose, cellulose, fructose lactose starch The monomer units of disaccharides and polysaccharides are joined by a COOOC structure called a glycosidic linkage between carbons 1 and 4 or 1 and 6 of adjacent monosaccharide units. The glycosidic linkages in disaccharides and polysaccharides are formed by a condensation reaction like the condensation reactions by which synthetic polymers are formed. A water molecule is released during the formation of each glyco- sidic bond from the reaction between the OOH groups of the monosaccharide monomers (Figure 10.15). Notice that maltose has two fewer hydrogen atoms and one less oxygen Unless otherwise noted, all content on this page is © Cengage Learning. Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it. 464 Chapter 10 | FUELS, ORGANIC CHEMICALS, AND POLYMERS Glycosidic linkage joins two monosaccharide units. CH2OH CH2OH CH2OH CH2OH O O O O H H H H H H H H H H H H 4 1 + 4 1 1 4 + H2O OH H OH H OH H O OH H HO OH HO OH HO OH H HO H HO H HO H HO glucose glucose maltose water Figure 10.15 Formation of maltose, a disaccharide, by condensation of glucose molecules. atom than the combined formulas of two glucose molecules. This difference arises be- cause a water molecule is a product of the condensation reaction. Polysaccharides contain many monosaccharide monomers joined together via glyco- sidic linkages into a very large polymer. Starches and cellulose are the most abundant natural polysaccharides. ­d-glucose is the monomer in each of these polymers, which can contain as many as 5000 glucose units. Conceptual Exercise 10.17 Sucrose Solubility On a chemical basis, explain why table sugar (sucrose) is soluble in water. 10-7b Polysaccharides: Starches and Glycogen Plant starch is stored in protein-covered granules until glucose is needed for synthesis of new molecules or for energy production. If these granules are ruptured by high tempera- ture, they yield two starches—amylose and amylopectin. Natural starches contain about 75% amylopectin and 25% amylose, both of which are polymers of glucose units joined by glycosidic linkages. Structurally, amylose is a condensation polymer with an average of about 200 glucose monomers per molecule arranged in a straight chain, like pearls Amylose turns blue-black when on a necklace. Amylopectin is a branched-chain polymer analogous to the branched- tested with iodine solution, chain synthetic polymers discussed earlier. A typical amylo­pectin molecule has about whereas amylopectin turns red. 1000 glucose monomers arranged into branched chains. The branched chains of glucose units give amylopectin properties different from those of the unbranched amylose. The main difference is their water solubilities. A family of enzymes called amylases helps to break down starches sequentially into a mixture of small branched-chain polysaccharides called dextrins and ultimately into glucose. Dextrins are used as food additives and in mucilage, paste, and finishes for paper and fabrics. In animals, glycogen serves the same storage function as starch does in plants. Glycogen is stored in the liver and muscle tissues and provides glucose for “instant” Animals store energy as fats rather than carbohydrates energy until the process of fat metabolism can take over and serve as the energy source because fats have more energy ( Sec. 4-11). The chains of d-glucose units in glycogen are more highly branched than per gram. those in amylopectin. 10-7c Cellulose, a Polysaccharide Cellulose is the most abundant organic compound on Earth, found as the woody part of Paper and cotton are nearly trees and the supporting material in plants and leaves. Cotton is the purest natural form pure cellulose. of cellulose. Like amylose, cellulose is composed of d-glucose monomer units. The Unless otherwise noted, all content on this page is © Cengage Learning. Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.  10-7 Biopolymers: Polysaccharides and Proteins 465 Biophoto Associates/Science Source Figure 10.16 A portion of one polymer chain in cellulose. About 280 glucose units are bonded together to form a chain. Chains lie parallel to each other and are held together by hydrogen bonds. Glucose monomer units are highlighted in pink. H atoms are not shown. Parallel strands of cellulose in a difference between the structures of cellulose and amylose lies in the orientation of the plant fiber. glycosidic linkages between the glucose monomer units. In cellulose, the OOH groups at carbons 1 and 4 are in the trans position, so the glycosidic linkages between glucose units alternate in direction; thus, every other glucose unit is turned over (Figure 10.16). In amylose, the OOH groups at carbons 1 and 4 are in the cis position, so all the glyco- sidic linkages are in the same direction. This subtle structural difference allows humans to digest starch, but not cellulose; we lack the enzyme necessary to break the trans gly- cosidic linkages in cellulose. However, termites, a few species of cockroaches, and rumi- nant mammals such as cows, sheep, goats, and camels do have the proper internal chemistry for this purpose. Because cellulose is so abundant, it would be advantageous if humans could use it, as well as starch, for food. Conceptual Exercise 10.18 Digestion of Cellulose Explain why humans cannot digest cellulose. Consult a reference on the Internet and ex- plain why ruminant animals can digest cellulose. Conceptual Exercise 10.19 What If Humans Could Digest Cellulose? Think of some of the implications if humans could digest cellulose. What would be some desirable consequences? What would be some undesirable ones? 10-7d Amino Acids and Proteins An amino acid contains a carboxylic acid group and an amine group. Proteins are co- polymers of amino acids. The 20 naturally occurring amino acids from which proteins are made have the general formula Side chain R O Carboxylic acid group H 2N C C OH Amine H α carbon group They are described as α-amino acids because the amine, ONH2, group is attached to the alpha (𝛂) carbon, the first carbon next to the carboxylic acid, OCOOH, group. As shown in Table 10.8, the amino acids differ in that each has a different R group, called a side chain. Glycine, the simplest amino acid, has just hydrogen as its R group. Note from the table that some amino acid R groups contain only carbon and hydrogen, while others contain carboxylic acid, amine, or other functional groups. The amino acids are grouped in Table 10.8 according to whether the R group is nonpolar, polar, acidic, or basic. Each amino acid has a three-letter abbreviation for its name, also given in the table. Unless otherwise noted, all content on this page is © Cengage Learning. Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it. 466 Chapter 10 | FUELS, ORGANIC CHEMICALS, AND POLYMERS Table 10.8  Common l-Amino Acids Found in Proteins† Name and Name and Abbreviation Structure Abbreviation Structure Nonpolar R groups Glycine H CH COOH *Isoleucine CH3 CH2 CH CH COOH Gly Ile NH2 CH3 NH2 Alanine CH3 CH COOH Proline H 2C CH2 Ala Pro NH2 H 2C CH COOH N H *Valine CH3 CH CH COOH *Phenylalanine Val Phe CH2 CH COOH CH3 NH2 NH2 *Leucine CH3 CH CH2 CH COOH *Methionine CH3 S CH2CH2 CH COOH Leu Met CH3 NH2 NH2 *Tryptophan CH2 CH COOH Trp NH2 N H Polar but neutral R groups Serine Ser HO CH2 CH COOH Asparagine H2N C CH2 CH COOH Asn NH2 O NH2 *Threonine CH3 CH CH COOH Glutamine H2N C CH2CH2 CH COOH Thr Gln OH NH2 O NH2 Cysteine HS CH2 CH COOH Tyrosine CH2 CH COOH Cys Tyr NH2 NH2 HO Acidic R groups Basic R groups Glutamic acid HO C CH2CH2 CH COOH *Lysine H2N CH2CH2CH2CH2 CH COOH Glu Lys O NH2 NH2 Aspartic acid HO C CH2 CH COOH ‡Arginine H2N C NH CH2CH2CH2 CH COOH Asp Arg O NH2 NH NH2 *Histidine CH2 CH COOH His NH2 N N H *Essential amino acids that must be part of the human diet; histidine is essential to juveniles, but not adults. The other amino acids can be synthesized by the body. †The R group in each amino acid is highlighted. ‡Growing children also require arginine in their diet. Unless otherwise noted, all content on this page is © Cengage Learning. Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.  10-7 Biopolymers: Polysaccharides and Proteins 467 Conceptual Exercise 10.20 Hydrogen Bonding Between Amino Acids in Proteins Choose two amino acids from Table 10.8 whose R groups can hydrogen-bond with one another if they were close together in a protein chain or in two adjacent protein chains. Then choose two whose R groups would not hydrogen-bond. Like nylon, proteins are polyamides. The amide bond in a protein is formed by the condensation polymerization reaction between the amine group of one amino acid and the carboxylic acid group of another. In proteins, the amide linkage is called a peptide linkage or peptide bond. A relatively small amino acid polymer (up to about 50 amino acids) is known as a polypeptide. Proteins contain hundreds to thousands of amino acids bonded together. Peptide linkage (bond) R1 O R2 O R1 O R2 O H 2N C C OH + H N C C OH H 2N C C N C C OH + H2O H H H H H H amino acid 1 amino acid 2 dipeptide Any two amino acids can react to form two different dipeptides, depending on which amine and acid groups react from each amino acid. For example, glycine and alanine can react and join in either of these two ways: H O H O H O H O H2N C C OH + H N C C OH H 2N C C N C C OH + H2O H H CH3 H H CH3 glycine alanine Peptide glycylalanine linkage Peptide linkage H O H O H O H O H 2N C C OH + H N C C OH H2N C C N C C OH + H2O CH3 H H CH3 H H alanine glycine alanylglycine Either dipeptide can react with another amino acid at each end. The extensive chains of amino acid units in proteins are built up by such condensation polymerization reactions. Polypeptide chains are named by starting at the ONH2 end and naming each amino acid (with a “yl” ending) until the OCOOH group is reached. Thus, as shown above, gly- cylalanine is different from alanylglycine. All proteins, no matter how large, have a peptide backbone of amino acid units co- valently bonded to each other through peptide linkages. H H O H O H O H O H O N C C N C C N C C N C C N C C N R1 H R2 H R3 H R4 H R5 H peptide linkages As the number of amino acids in the chain increases, the number of variations quickly in- creases to a degree of complexity not usually found in synthetic polymers. As we have just seen, two different dipeptides can form by reacting two different amino acids. Six tripeptides Unless otherwise noted, all content on this page is © Cengage Learning. Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it. 468 Chapter 10 | FUELS, ORGANIC CHEMICALS, AND POLYMERS are possible if each of three different amino acids is used only once. For example, phenyl­ Peptide bond alanine, Phe; alanine, Ala; and serine, Ser can be linked in these combinations: α Phe-Ala-Ser Ser-Ala-Phe Ala-Ser-Phe Phe-Ser-Ala Ser-Phe-Ala Ala-Phe-Ser α α If n different amino acids are present, the number of arrangements is n! (n ­factorial). For Serine four different amino acids, the number of different tetrapeptides is 4! = 4 × 3 × 2 × 1 = 24. If all 20 naturally occurring amino acids were each used once to form all possible poly- Alanine peptides, there would be 20! = 2.43 × 1018 (2.43 quintillion) unique 20-monomer polypep- tide molecules. Because a protein chain can also include more than one molecule of a given amino acid, the number of possible combinations is astronomical. It is truly remarkable that of the many different proteins that could be made from a set of amino acids, a living cell Phenylalanine makes only the relatively small number of proteins it needs. The Ala-Phe-Ser tripeptide Problem-Solving Example 10.10 Peptides Using information from Table 10.8, draw the structural formula of the tripeptide represented by Ala-Ser-Gly. Name the tripeptide. Explain why it is a different compound from the tri- peptide with the amino acids joined in the order Gly-Ala-Ser. Result H O H O H O H2N C C N C C N C C OH CH3 H CH2OH H H Ala-Ser-Gly The name is alanylserylglycine. The structure Gly-Ala-Ser differs because the free ONH2 group is on the glycine part of the molecule and the free OCOOH group is on the serine part of the molecule. Analyze  The abbreviated name begins with the free H2NO group and proceeds to the free OCOOH group. Amino acids are connected by peptide bonds. The name of a polypeptide is derived from the names of the monomer amino acids. Plan  Write the structures for alanine, serine, and glycine. Connect the structures by forming peptide bonds (removing HOH). Name the polypeptide starting from the left (ONH2) end, replacing “ine” with “yl” in each name except the last. Draw the structure of Gly-Ala-Ser and describe how it differs from Ala-Ser-Gly. Execute  See Result above. Writing the structure of Gly-Ala-Ser shows how the two tripeptides are different. H O H O H O H2N C C N C C N C C OH H H CH3 H CH2OH Gly-Ala-Ser Problem-Solving Practice 10.10 Name and draw the structural formula of the tetrapeptide Lys-Phe-Ser-Ala. Exercise 10.21 Peptide Sequences Draw the structural formula of the tetrapeptide Ala-Ser-Phe-Cys. Identify each amino acid side chain as nonpolar, polar but neutral, acidic, or basic. Unless otherwise noted, all content on this page is © Cengage Learning. Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.  10-7 Biopolymers: Polysaccharides and Proteins 469 CNRI/Science Photo Library/Science Source The change in structure of Science Source hemoglobin that causes sickle- cell anemia answers the question, “How can a disease (a) Normal cells (b) Sickled cells be caused or cured by a tiny Figure 10.17 Red blood cells. Changing one amino acid in the primary protein structure of hemoglobin change in a molecule?” that was causes the disease sickle-cell anemia; symptoms are fatigue and pain. posed in Chapter 1 ( Sec. 1-1). 10-7e Primary, Secondary, and Tertiary Protein Structure The three-dimensional shape of a protein, and consequently the function it carries out in a living organism, is determined by the protein’s primary structure—the sequence of amino acids along the polymer chain. The sequence of amino acids is reflected in the order of the R groups along the backbone. Even one amino acid out of place can create dramatic changes in the shape of a protein, which can lead to serious medical conditions. For example, the function of hemoglobin is to carry oxygen in red blood cells. Altering the primary structure of hemoglobin causes the disease sickle-cell anemia. Glutamic acid, the sixth amino acid in a 146–amino acid chain in hemoglobin, is replaced by va- line. Replacement of the carboxylic acid side chain of glutamic acid with the nonpolar side chain of valine (Table 10.8) disturbs the attractions between hemoglobin molecules and causes them to gather into fibrous chains that distort the red blood cells into a sickle shape (Figure 10.17). In addition to the sequence of amino-acid side chains, protein molecules have secondary structure, regular, recurring structural patterns held in place by hydrogen bonding. Figure 10.18 shows the two major types of secondary protein structure: the alpha-helix (α-helix) and the beta-pleated sheet (β-pleated sheet). The α-helix occurs Planar peptide linkages make these regions flat. Alpha-helix. Hydrogen bonds hold a protein chain in a spiral (helix) structure. Beta-pleated sheet. Hydrogen bonds hold adjacent protein chains in a puckered (pleated) sheet. Figure 10.18 Secondary protein structures: alpha-helix and beta-pleated sheet. Unless otherwise noted, all content on this page is © Cengage Learning. Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it. 470 Chapter 10 | FUELS, ORGANIC CHEMICALS, AND POLYMERS within a single protein chain. The β-pleated sheet involves two or more adjacent sections of protein chains; the two adjacent sections may be in separate molecules or within the same molecule where a protein chain folds so that different sections of the chain are par- allel. In the alpha-helix, hydrogen bonding occurs between a hydrogen atom in an NOH bond in one peptide linkage with a lone electron pair on a CPO oxygen of a peptide bond four amino acid units farther down the backbone (Figure 10.18). In effect, the hy- Wool is primarily the protein drogen in the hydrogen bond “looks over its shoulder,” causing the protein to curl into a keratin, which has an alpha- helix, much like the coiling of a spring. In the alpha-helix, the R groups on the amino helix secondary structure. acid units are on the outside of the helix. Fibroin, the principal protein in Hydrogen bonding in the beta-pleated sheet occurs between the peptide backbones silk, is largely beta-pleated sheets. of neighboring protein chains, creating a zigzag pattern resembling a pleated sheet with the R groups above and below the sheet (Figure 10.18). The reason for the pleated, zig- zag structure is that the six atoms involved in a peptide bond all are in the same plane. The peptide bond is a resonance hybrid of these two structures: O O− C C C C + N C N C H H Because of the double bond in the right-hand structure, there is no free rotation around the CON bond and both the C and N atoms have triangular-planar geometry. Thus, the only place where there can be a bend in a polypeptide chain is at the carbon atom to which the R group is attached and the sheets are pleated. In many proteins, the backbone is folded into a globular structure as shown in Fig- ure 10.19. Within the globular structure there may be regions of α-helix and β-pleated sheet. The overall three-dimensional arrangement that accounts for all the twists and turns and folding of a protein is called its tertiary protein structure. The twists and turns of the tertiary structure result in a protein molecule of maximum stability. Tertiary structure is determined by interactions among the side chains strategically placed along the backbone of the chain. These interactions include noncovalent forces of attraction and covalent bonding, as listed in this table and illustrated in Figure 10.20. Noncovalent Attractions Covalent Bonds Hydrogen bonding between side-chain Disulfide bonds, OSOSO groups Coordinate covalent bonding Hydrophobic (water-hating) interactions Coordinate covalent bonding between between metal ions and lone between nonpolar side-chain hydrocarbon metal ions and electron pairs of side-chain pairs of electrons is discussed in groups N and O atoms detail in Sections 14-9 and 20-6. Electrostatic attractions between ONH3+and OCOO− side-chain groups Beta-pleated sheet Alpha-helix Figure 10.19 Protein folding in the enzyme chymotrypsin. Only the polypeptide backbone is shown. Alpha- helix regions are shown in blue, beta- Randomly coiled pleated sheet regions are shown in region green, and randomly coiled (neither alpha-helix nor beta-pleated sheet) regions are shown in copper. Unless otherwise noted, all content on this page is © Cengage Learning. Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.  10-7 Biopolymers: Polysaccharides and Proteins 471 Metal ion Hydrophobic Disulfide Electrostatic coordination interactions bond attraction CH3 CH2 CH3 O- CH O– S S C C O O M C O 2+ HC CH2 CH2 CH2 O CH3 C CH2 H N H CH2 C H CH3 (CH2)4 O O- H + H3C C CH2 N H H CH3 CH3 (CH2)4 H O N