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Unformatted text preview: Chapter Twenty-Five SYNTHETIC AND NATURAL ORGANIC POLYMERS • • • Synthetic Organic Polymers Proteins Nucleic Acids SYNTHETIC ORGANIC POLYMERS STUDY OBJECTIVES 1. 2. 3. Define monomer and give several examples of addition polymers. Define copolymer and give several examples of condensation polymers. Describe the steps in the addition polymerization process. Polymers. The word polymer means "many parts." A p olymer is a compound with an unusually high molecular mass, consisting of a large number of small molecular units that are linked together. The small unit that is repeated many times is called a m onomer . A typical polymer molecule contains a chain of monomers several thousand units long. Polymers are often called macromolecules. Proteins, nucleic acids, carbohydrates, and rubber are natural polymers. Synthetic polymers such as nylon, polyester, and polyethylene are organic compounds. Addition Polymers. Addition polymers are made by adding monomer to monomer until a long chain is produced. Ethylene and its derivatives are excellent monomers for addition polymers. In an addition reaction, the polymerization process is initiated by a radical. When ethylene is heated to 250° C under high pressure (1000– 3000 atm) in the presence of a little oxygen or benzoyl peroxide (the initiator), addition polymers with molecular masses of about 30,000 amu are obtained. This reaction is represented by: HH HHH HHH HH | | | | | | | | | | n C C → —C—C—C—C—C—C—C—C— | | | | | | | | | | HH HHH HHH HH ethylene a segment of polyethylene The general equation for addition polymerization is: HH HH | | | | n C C → —C— C— | | | | HH HHn monomer repeating unit 4 78 Back Forward Main Menu TOC Study Guide TOC Textbook Website MHHE Website Synthetic and Natural Organic Polymers / 4 79 Polyethylene is an example of a h omopolymer , which is a polymer made up of only one type of monomer. Substitution of one or more hydrogen atoms in ethylene with Cl atoms, phenyl groups , acetate, cyano groups, and F atoms provides a wide selection of monomers from which to make various homopolymers. For example, substitution of a Cl atom for an H atom in ethylene gives the monomer called vinyl chloride, CH2 CHCl. Polymerization of vinyl chloride yields the polymer, polyvinyl chloride. HH HH | | | | n C C → —C— C— | | | | H Cl H Cl n vinyl chloride polyvinyl chloride monomer repeating unit Table 25.1 in the text gives the names, structures, and uses of a number of monomers and addition polymers. Addition Polymerization. The addition polymerization process occurs by several steps which are summarized below. The first step is called initiation . This is followed by a chain growth process, and finally a termination reaction. 1. Initiaition. Polymerization is initiated by a radical. A radical (also called a free radical) is a species which has an unpaired electron. The symbol for a radical contains the usual letters for the elements followed by a dot to represent the unpaired electron. CH3 . is the symbol for a methyl radical. The letter R is the general symbol for an alkyl group and R. for an alkyl radical. In a polymerization process, first the initiator molecule is dissociated by heating to yield two radicals. Then the radical adds to an ethylene molecule which generates a new radical. R—R → 2R · R . + CH2 CH2 → R —CH2 —CH2 · 2. Chain Growth. Next, the free radical formed above can add to another molecule of ethylene. R —CH2 —CH2 · + CH 2 CH2 → R —CH2 —CH2 —CH2 —CH2 · The length of the carbon chain grows rapidly as the last free radical formed reacts with yet another ethylene molecule, and so on. R —(CH2 —CH2 )n —CH2 —CH2 · 3. Termination. The polymerization process continues until a termination reaction occurs. When the radical ends of two chains meet they may combine. When this happens there is no new radical formed and the chain lengthening process ceases. Of course the result of this termination is the formation of a molecule of polyethylene which may contain up to 800 carbon atoms. R —(CH2 —CH2 )n —CH2 —CH2 · + · CH2 —CH2 —(CH2 —CH2 )n —R → R —(CH2 —CH2 )n —CH2 —CH2 —CH2 —CH2 —(CH2 —CH2 )n —R Condensation Polymers. C opolymers are polymers that contain two or more different monomers. When monomers A and B are linked by condensation reactions a uniform copolymer, —ABABAB— can be formed. Nylon and polyesters, such as the well-known Dacron, are copolymers. Polyester is made by an esterification reaction. When one monomer is an alcohol and the other is a carboxylic acid, they can be joined by an esterification reaction. The alcohol and the acid both must contain two functional groups. The monomers in polyester are the dicarboxylic acid called phthalic acid, and the dialcohol, ethylene glycol. Back Forward Main Menu TOC Study Guide TOC Textbook Website MHHE Website 4 80 / Synthetic and Natural Organic Polymers O HO O C C OH HO C H 2 C H2 phthalic acid OH ethylene glycol Condensation reactions differ from addition reactions in that the former always result in the formation of a small molecule such as water. Polyesters are produced from the esterification reaction between an alcohol and an acid. When phthalic acid and ethylene glycol react to form an ester, the first products are: O C HO O C OCH2 CH2 OH + H2 O This molecule can react further from both ends. When this product reacts with another molecule of the diacid, the polymer chain grows longer. O C HO O C O OCH2 CH2 O O C C OH + H2 O Segment of a condensation polymer chain The general formula for this polyester is: O O C C OCH2 CH2 O— n _______________________________________________________________________________ EXAMPLE 25.1 Monomers and Polymers Write the formulas of the monomers used to prepare the following polymers: a. Teflon b. Polystyrene c. PVC •Method of Solution Refer to Table 25.1 of the text. a. Teflon is an addition polymer with the formula –( CF2 —CF 2 )–n . It is prepared from the monomer tetrafluoroethylene (CF2 CF 2 ). b. The monomer used to prepare polystyrene is styrene. ( CH CH2 ) n CH polystyrene CH2 styrene c. Polyvinylchloride is prepared by the successive addition of vinyl chloride molecules, CH2 CHCl. _______________________________________________________________________________ Back Forward Main Menu TOC Study Guide TOC Textbook Website MHHE Website Synthetic and Natural Organic Polymers / 4 81 EXERCISES 1. 2. 3. List three steps occurring during addition polymerization. What monomer is used to make Teflon ( CF2 —CF 2 )n ? Is Teflon a homopolymer or a copolymer? PROTEINS STUDY OBJECTIVES 1. 2. 3. Write a general formula for an amino acid. Describe the condensation reaction between two amino acids that result in the formation of a dipeptide. Discuss the terms used to describe the four levels of protein structure. Proteins. Proteins are truly giant molecules having molecular masses that range from about 10,000 to several million amu. Proteins play many roles in living organisms where they function as catalysts (enzymes), transport molecules (hemoglobin), contractile fibers (muscle), protective agents (blood clots), hormones (chemical messengers), and structural members (feathers, horn, nails). The word protein comes from the Greek word proteios, meaning "first." From this partial list of functions it is easy to see why proteins occupy "first place" among biomolecules in their importance to life. Amino Acids. Even though each protein is unique, all proteins are built from the same set of amino acids. An amino acid consists of an amino group, a carboxylic acid group, a hydrogen atom, and a distinctive Rgroup, all bonded to the same carbon atom. HO | || H2 N—C—C—OH | R All amino acids in proteins have a common structural feature. This is the attachment of the amino group to the carbon atom adjacent to the carboxylic acid group. The R-group is different in each amino acid, and some 20 different R-groups are found in the proteins from natural sources. The structural formulas of the amino acids are shown in Table 25.2 (text). Amino acids in solution at near neutral pH exist as dipolar ions. This form results from the transfer of a proton from the carboxylic acid group to the basic amine group HO | || +H N—C—C—O– 3 | R In proteins the amino acid units are hooked together to form a polypeptide chain. The carboxyl group of one amino acid is joined to the amino group of another amino acid by the formation of a peptide bond. Back Forward Main Menu TOC Study Guide TOC Textbook Website MHHE Website 4 82 / Synthetic and Natural Organic Polymers HO HO HO HO | || | || | || | || +H N—C—C—O– + +H N—C—C—O– → +H N—C—C—NH—C—C—O – + H O 3 3 3 2 | | | | R1 R2 R1 R2 This type of reaction is another example of a condensation reaction. The new C—N covalent bond is called a peptide bond or an amide bond. The amide functional group is present in all proteins: peptide bond O C NH amide group The molecule above in which two amino acids are joined is called a dipeptide. Peptides are structures intermediate in size between amino acids and proteins. The term polypeptide refers to long molecular chains containing many amino acid units. An amino acid unit in a polypeptide chain is called a residue. Structure of Proteins. Proteins are so complex that four levels of structural features have been identified. The structure of proteins is extremely important in determining just how efficiently and effectively a protein will function. A stretched-out or unfolded polypeptide chain does not exhibit biological activity, and is said to be denatured. The four levels of protein structure are summarized below. 1. 2. 3. 4. Back The Primary Structure. Each protein has a unique amino acid sequence of its polypeptide chain. It is the amino acid sequence that distinguishes one protein from another. Proteins differ in the numbers and kinds of amino acids, but especially in the sequence of amino acid residues. The Secondary Structure. This refers to the spatial relationship of amino acid units that are close to one another in the sequence. A configuration that appears in many proteins is the α -helix shown in Figure 25.13 (textbook). In this configuration the polypeptide is coiled much like the arrangement of stairs in a spiral staircase. The tightly coiled polypeptide chain forms the inner part of the spiral stairway, and the R groups extend outward forming a helical pattern. The figure shows that the α -helix is stabilized by the presence of hydrogen bonds (dashed lines) between the C O and NH groups in the peptide chains. The CO group of each amino acid is hydrogen bonded to the NH group of the amino acid that is located four amino acids ahead in the sequence. Thus amino acids spaced four apart in the sequence are actually close to one another due to the coiled or spiral arrangement. The α -helix is the main structural feature of the oxygen-storage protein, myoglobin, and of many other proteins. The presence of this feature in a polypeptide chain is shown in Figure 25.14 (text). The β-pleated sheet is another common protein structure. In this structure a polypeptide chain interacts strongly with adjacent chains by forming many hydrogen bonds (Figure 25.15 text). The Tertiary Structure. Myoglobin like many other proteins is a globular protein. The polypeptide chain is folded into a compact globular shape. The folding of the chain results in some amino acid units being in very close proximity to each other even though they are widely separated in the amino acid sequence. The term tertiary structure refers to the spatial relationship of amino acid units that are far apart in the sequence, or more simply, to just its three-dimensional structure. In myoglobin, for example, the tertiary structure is a unique three-dimensional shape resulting from the folding of the polypeptide chain. The folding takes place quite naturally in aqueous medium due to the interactions of hydrophobic and hydrophilic R groups with water. The tertiary structure is stabilized by hydrogen bonding, dispersion forces, and ionic forces. The Quaternary Structure. Proteins that consist of more than one polypeptide chain exhibit an additional level of structural organization called the quaternary structure. This structural feature involves the way in which separate chains fit together. Hemoglobin, the oxygen-carrying molecule of the blood, exhibits a quaternary structure (Figure 25.19 in the textbook). It consists of four separate polypeptide chains or subunits (labeled α 1 , α 2 , β1 , β2 ). The quaternary structure results from interaction between chains. Ionic forces and hydrogen bonds are important in holding the subunits together. Forward Main Menu TOC Study Guide TOC Textbook Website MHHE Website Synthetic and Natural Organic Polymers / 4 83 _______________________________________________________________________________ EXAMPLE 25.2 Amino Acids Find and name five amino acids in Table 25.2 (textbook) that have polar R groups. •Method of Solution Recall that polar groups are those that have relatively large electronegativity differences between bonded atoms. Thus, —COOH, —OH, and —SH are polar R groups. Answer: The R groups in aspartic acid and glutamic acid contain carboxylic acid groups. The R groups in serine and threonine contain hydroxyl groups. And the R group in cysteine contains a polar —SH group. _______________________________________________________________________________ EXAMPLE 25.3 A Polypeptide Chain Sketch a portion of a polypeptide chain consisting of the amino acids cysteine, glycine, valine, and phenylalanine. Point out the peptide bonds and amide groups. •Method of Solution The main backbone of a polypeptide chain is made up of carbon atoms, and the amide group repeating alternately along the chain. The abbreviation for the chain is cys—gly—val—phe. R CH O R O C NH CH C NH amide group amide group Table 25.2 (text) gives the structures of the amino acids. Substitute for each R group shown above, the distinctive R groups of the four amino acids. The chain structure will be: O O O O || || || || —CH—C—NH—CH—C—NH—CH—C—NH—CH—C—NH— | | | | CH 2 H C H—CH 3 CH2 | | | SH CH3 cys gly val phe There are four peptide bonds. They are the C—N bonds. Each –CO—NH– is an amide group. _______________________________________________________________________________ EXAMPLE 25.4 Tertiary Structure of Proteins What kinds of forces stabilize the tertiary structures of proteins? •Method of Solution The term tertiary structure is given to the folded three-dimensional structure. The polypeptide chain folds into a specific three-dimensional structure under the influence of hydrophobic and hydrophilic interactions. The hydrophilic R groups (polar or ionic groups are attracted to water) are spread uniformly over the outside surface of the folded polypeptide chain where they can interact with water via hydrogen bonding and ion-dipolar Back Forward Main Menu TOC Study Guide TOC Textbook Website MHHE Website 4 84 / Synthetic and Natural Organic Polymers interactions. The chain folds in such a way that the hydrophobic R groups (nonpolar groups are repelled by water) appear on the "inside" of the molecule where water molecules cannot reach. _______________________________________________________________________________ EXERCISES 4. 5. 6. 7. 8. What is an amino acid? Sketch the dipolar ion of alanine. What is an amide group and a peptide bond? What is the primary structure of a protein? What is a denatured protein? NUCLEIC ACIDS STUDY OBJECTIVES 1. 2. 3. Describe the composition of nucleic acids. Distinguish chemical and structural differences between DNA and RNA. Draw structures of nucleotides and indicate where they link together to form strands of nucleic acids. Components of DNA and RNA. The chemical composition of the cell nucleus was first studied in the 1860s by Friedrich Miescher. He found the major components to be protein and a new material not previously isolated. This material was found to be acidic, and so it was referred to as nucleic acid. Nucleic acids are now known to be giant molecules with molecular masses in the range 1 to 10 billion amu. These molecules carry information in the form of the genetic code. Enough information is stored in nucleic acid molecules to allow the complete assembly of an entire organism. The nucleic acid molecule called DNA carries this information from generation to generation. Hydrolysis of nucleic acid showed that it is composed of one part phosphoric acid, one part sugar, and one part nitrogen base. One of two sugars are present—ribose or deoxyribose. Five different nitrogen bases are found in nucleic acids. Their names are adenine, thymine, guanine, cytosine, and uracil (Figure 25.17 text). Two types of nucleic acids are recognized. These are called DNA and RNA. The compositions of DNA and RNA are quite similar, but they differ in two significant ways. DNA contains the sugar deoxyribose and is called deoxyribonucleic acid. RNA contains the sugar ribose, hence the name ribonucleic acid. The second difference is that DNA contains the four bases adenine, thymine, guanine, and cytosine, while RNA contains adenine, uracil, guanine, and cytosine. DNA contains thymine but no uracil, whereas RNA contains uracil but no thymine. Table 25.1 summarizes the building blocks of DNA and RNA and gives useful abbreviations. HOCH 2 H H O HOCH 2 OH H H H OH OH R ibose Back Forward Main Menu H O OH H H OH H Deoxyribose TOC Study Guide TOC Textbook Website MHHE Website Synthetic and Natural Organic Polymers / 4 85 Table 25.1 The Component Parts of DNA and RNA. _________________________________________________ DNA RNA _________________________________________________ Acid: phosphoric acid (P) phosphoric acid (P) Sugar: deoxyribose (D) ribose (R) N bases:adenine (A) adenine (A) thymine (T) uracil (U) guanine (G) guanine (G) cytosine (C) cytosine (C) _________________________________________________ Nucleotides. The repeating unit in nucleic acids is called a nucleotide. It is a combination of a phosphate group, a five-carbon sugar, and a nitrogen base. See Figure 25.18 (text) for the full structure of the nucleotide, deoxyadenosine monophosphate (dAMP), which contains the sugar deoxyribose, and the base adenine. Figure 25.1 below shows the structure of the nucleotide containing the base cytosine, the sugar ribose and the phosphate group. It is named cytosine monophosphate (CMP). NH 2 O O P N O CH 2 O N H H OH O H O OH H Figure 25.1 The molecular structure of the nucleotide cytosine monophosphate (CMP). The phosphoric acid groups of nucleotides are quite acidic, and at pH 7 these groups exist mainly as the dianion as shown. Nucleic Acids. A strand of DNA or RNA is constructed by linking the nucleotides together with a bond from the sugar unit of one nucleotide to the phosphate unit of another nucleotide. Such a strand of DNA is represented in abbreviated form below. To simplfy DNA and RNA structures we will use the abbreviations in Table 25.1: P = phosphate, D = deoxyribose, and A, G, T, and C for the bases. / P \ D—A / P \ D—G / P \ D—T / P \ D—C / P \ Back Forward Main Menu TOC Study Guide TOC Textbook Website MHHE Website 4 86 / Synthetic and Natural Organic Polymers In the 1940s, Edwin Chargaff studied the composition of DNA. His analysis of the base composition of DNA showed that the amount of adenine (A) always equaled that of thymine (T), and that the amount of guanine (G) equaled that of cytosine (C). These relations became known as Chargaff's rules. Watson and Crick in 1953 proposed a two stranded structure for DNA which provided an explanation of Chargaff's rules. The two-stranded structure can be shown as follows: / \ P P \ / D—C · · · G—D / \ P P \ / D—A · · · T—D / \ P P \ / D—G · · · C—D / \ P P \ / D—T · · · A—D / \ P P \ / Adenine in one strand is always paired with thymine in the other strand. Guanine is always paired with cytosine. The two strands are not identical, rather they are complementary. Base pairing and the resulting association of the two strands are the result of hydrogen bonding. Hydrogen atoms in a base in one strand form hydrogen bonds to oxygen and nitrogen atoms of a base attached to the other strand (see Figure 25.19(a) in textbook). X-ray data suggested that DNA had the helical structure as shown in Figure 25.19(b) of the text. RNA, on the other hand, does not follow the base-pairing rules. X-ray data and other evidence ruled out a double-helical structure for RNA. RNA is single stranded. _______________________________________________________________________________ EXAMPLE 25.5 Nucleotide Structures Sketch the structure of the nucleotide containing uracil that appears in RNA. •Method of Solution Nucleotides from RNA contain ribose as the sugar and and a phosphate dianion. The structure of the base uracil is given in Figure 25.17 in the text. The phosphate group in bonded to the sugar which in turn is bonded to the nitrogen base, uracil. The structure is: O O O P O N O CH 2 H O H N H O H OH OH Phosphate unit Ribose unit Uracil unit _______________________________________________________________________________ Back Forward Main Menu TOC Study Guide TOC Textbook Website MHHE Website Synthetic and Natural Organic Polymers / 4 87 _______________________________________________________________________________ EXAMPLE 25.6 Base Pairing What types of forces cause base pairing in the double-stranded helical DNA molecule? •Method of Solution The N-bases thymine (T) and cytosine (C) in one strand of DNA form hydrogen bonds to the N-bases adenine (A) and guanine (G), respectively, in the other DNA strand. Hydrogen atoms that are covalently bonded to nitrogen carry a partial positive charge. These H atoms are attracted to lone electron pairs on oxygen and nitrogen atoms of another base. Since two complementary bases are attached to different strands, the hydrogen bonds hold the strands together. HN N N H δ+ N. N adenine . . .O δ+ .H. N O CH 3 N thymine _______________________________________________________________________________ EXERCISES 9. 10. 11. 12. 13. What is the 5-carbon sugar in DNA? In RNA? Name four nitrogen bases found in DNA. What type of bond is responsible for base pairing in DNA? Only DNA has base-pairing rules. Why doesn't RNA have base-pairing rules? What is the repeating unit in nucleic acids? ____________________________________________________________________________ PRACTICE TEST 1. 2. Sketch the structures of the monomers from which these polymers are formed. a. Cl H Cl H Cl H | | | | | | —C— C— C— C— C— C | | | | | | H CH 3 H CH 3 H C H 3 b. —CH2 —CCl 2 —CH2 —CCl 2 —CH2 —CCl 2 — Draw structures for the monomers used to make the following polyester. O O || || —C—(CH2 )4 —C—O—(CH2 )3 —O—n 3. 4. 5. Back Sketch the structure of the monomer of natural rubber. What chemical elements are found in proteins? List several functions of proteins in living systems. Forward Main Menu TOC Study Guide TOC Textbook Website MHHE Website 4 88 / Synthetic and Natural Organic Polymers 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. What is the role of enzymes in biochemical systems? Describe the structure of an amino acid. Describe a dipeptide. A polypeptide. Draw the structural formula of the tripeptide formed from the sequence of amino acids below. (See Table 25.2 of the textbook.) Label the peptide bonds and R groups. Ser—Cys—Lys Consider two polypeptide chains 1. Lue—Phe—Pro—Gly—Ala 2. Gly—Ser—Lys—Asp—Tyr a. Which would be more soluble in water? b. Which would be more soluble in a nonpolar solvent? Explain how the primary structure of a protein differs from the tertiary structure. List four differences between DNA and RNA. Sketch the structure of the nucleotide consisting of phosphate, deoxyribose, and adenine. What is the biological role of DNA? If the base sequence in one strand of DNA is A, T, G, C, T, then the base sequence in the complementary strand is __, __, __, __, __. ANSWERS Exercises 1. 2. 3. 4. Initiation, chain growth, and termination. CF 2 CF 2 a homopolymer An amino acid is a carboxylic acid that contains an amino group (—NH2 ) attached to the carbon atom adjacent to the carboxylic acid functional group (—COOH). 5. HO | || +H N—C—C—O– 3 | CH3 An amide group is a –CO—NH– group. The peptide bond is the C—N bond that links amino acids in a polypeptide or protein. The sequence of amino acids in a peptide chain. Denaturation is the loss of structure in a protien. The structure change may be a loss of secondary, tertiary, or quaternary structure. Sometimes the primary structure is lost. Deoxyribose. Ribose. Adenine, guanine, cytosine, and thymine. A hydrogen bond. RNA is single stranded, not double stranded. A nucleotide. 6. 7. 8. 9. 10. 11. 12. 13. Back Forward Main Menu TOC Study Guide TOC Textbook Website MHHE Website Synthetic and Natural Organic Polymers / 4 89 Practice Test 1. a. CH 3 CH 2. O O || || HO—C—(CH2 )4 —C—OH 3. CH 3 | C—CH CH2 4. 5. 6. 7. 8. 9. CHCl b. CH2 CCl 2 HOCH2 CH2 CH2 OH CH2 C, H, O, N, and S Catalysts, transport, contractile, protection, hormones, structural elements. Enzymes are catalysts. Amino acids consist of an amino group, a carboxylic acid group, a hydrogen atom, and R group all bonded to the same carbon atom. A dipeptide is two amino acids linked by a peptide bond. A polypeptide consists of many amino acid residues each linked to the next by peptide bonds. O O O || || || H2 N—CH—C—NH—CH—C—NH—CH—C—OH | ↑ | ↑ | CH2 CH2 CH2 | | | OH SH CH 2 | CH2 | NH2 ser cys lys 10. a. 2 b. 1 11. The primary structure of a protein refers to the number and the sequence of amino acids within the polypeptide chain. The chain twists and folds so that some amino acids far apart in sequence come into proximity with each other. The tertiary structure is the 3D structure that shows the folding of the polypeptide chain. 12. (1) RNA contains uracil but no thymine; DNA contains thymine but no uracil. (2) RNA contains ribose as the 5-carbon sugar; DNA contains deoxyribose. (3) RNA is single stranded; DNA is double helical. (4) DNA is found only in the nucleus; RNA is found outside the nucleus. 13. NH 2 N O O P O CH 2 O N H H H OH O N N H H 14. DNA is the molecule of heredity; it is responsible for passing genetic information from one generation to the next. 15. T, A, C, G, A _____________________________________________________________________________ Back Forward Main Menu TOC Study Guide TOC Textbook Website MHHE Website ...
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