(BQ) Part 2 book Introduction to general, organic and biochemistry has contents: Amines, aldehydes and ketones, carboxylic acids, carboxylic anhydrides, esters, and amides, nucleotides, nucleic acids, and heredity, biosynthetic pathways,...and other contents.
16 Amines Key Questions 16.1 What Are amines? 16.2 How Do We Name Amines? 16.3 What Are the Physical Properties of Amines? Image not available due to copyright restrictions 16.4 How Do We Describe the Basicity of Amines? 16.5 What Are the Characteristic Reactions of Amines? 16.1 What Are Amines? Carbon, hydrogen, and oxygen are the three most common elements in organic compounds Because of the wide distribution of amines in the biological world, nitrogen is the fourth most common element of organic compounds The most important chemical property of amines is their basicity Amines (Section 10.4B) are classified as primary (1°), secondary (2°), or tertiary (3°), depending on the number of carbon groups bonded to nitrogen H CH3 CH3 NH2 CH3 N CH3 CH3 N CH3 Methylamine (a 1° amine) Dimethylamine (a 2° amine) Trimethylamine (a 3° amine) Online homework for this chapter may be assigned in GOB OWL 442 ■ Chapter 16 Amines Chemical Connections 16A Amphetamines (Pep Pills) Amphetamine, methamphetamine, and phentermine—all synthetic amines—are powerful stimulants of the central nervous system Like most other amines, they are stored and administered as their salts The sulfate salt of amphetamine is named Benzedrine, the hydrochloride salt of the S enantiomer of methamphetamine is named Methedrine, and the hydrochloride salt of phentermine is named Fastin These three amines have similar physiological effects and are referred to by the general name amphetamines Structurally, they have in common a benzene ring with a three-carbon side chain and an amine nitrogen on the second carbon of the side chain Physiologically, they share an ability to reduce fatigue and diminish hunger H N NH2 Amphetamine (Benzedrine) by raising the glucose level of the blood Because of these properties, amphetamines are widely prescribed to counter mild depression, reduce hyperactivity in children, and suppress appetite in people who are trying to lose weight These drugs are also used illegally to reduce fatigue and elevate mood Abuse of amphetamines can have severe effects on both body and mind They are addictive, concentrate in the brain and nervous system, and can lead to long periods of sleeplessness, loss of weight, and paranoia The action of amphetamines is similar to that of epinephrine (Chemical Connections 16E), the hydrochloride salt of which is named adrenaline NH2 CH3 (S)-Methamphetamine (Methedrine) Phentermine (Fastin) Amines are further classified as aliphatic or aromatic An aliphatic amine is one in which all the carbons bonded to nitrogen are derived from alkyl groups An aromatic amine is one in which one or more of the groups bonded to nitrogen are aryl groups Aliphatic amine An amine in which nitrogen is bonded only to alkyl groups or hydrogens Aromatic amine An amine in which nitrogen is bonded to one or more aromatic rings H NH2 Aniline (a 1° aromatic amine) Heterocyclic amine An amine in which nitrogen is one of the atoms of a ring Heterocyclic aromatic amine An amine in which nitrogen is one of the atoms of an aromatic ring CH3 N CH3 CH2 N CH3 N-Methylaniline (a 2° aromatic amine) Benzyldimethylamine (a 3° aliphatic amine) An amine in which the nitrogen atom is part of a ring is classified as a heterocyclic amine When the ring is saturated, the amine is classified as a heterocyclic aliphatic amine When the nitrogen is part of an aromatic ring (Section 13.1), the amine is classified as a heterocyclic aromatic amine Two of the most important heterocyclic aromatic amines are pyridine and pyrimidine, in which nitrogen atoms replace first one and then two CH groups of a benzene ring Pyrimidine and purine serve as the building blocks for the amine bases of DNA and RNA (Chapter 25) N N N N H H Pyrrolidine Piperidine (heterocyclic aliphatic amines) N N N N H Pyridine Pyrimidine Imidazole (heterocyclic aromatic amines) N N N H Purine N H Pyrrole 16.1 What Are Amines? ■ 443 Example 16.1 Structure of Amines How many hydrogen atoms does piperidine have? How many hydrogen atoms does pyridine have? Write the molecular formula of each amine Strategy Remember that hydrogen atoms bonded to carbon are not shown in line-angle formulas To determine the number of hydrogens present, add a sufficient number to give four bonds to each carbon and three bonds to each nitrogen Solution Piperidine has 11 hydrogen atoms, and its molecular formula is C 5H 11N Pyridine has hydrogen atoms, and its molecular formula is C 5H 5N Problem 16.1 How many hydrogen atoms does pyrrolidine have? How many does purine have? Write the molecular formula of each amine Chemical Connections 16B Alkaloids Alkaloids are basic nitrogen-containing compounds found in the roots, bark, leaves, berries, or fruits of plants In almost all alkaloids, the nitrogen atom is part of a ring The name “alkaloid” was chosen because these compounds are alkali-like (alkali is an older term for a basic substance) and react with strong acids to give water-soluble salts Thousands of different alkaloids, many of which are used in modern medicine, have been extracted from plant sources When administered to animals, including humans, alkaloids have pronounced physiological effects Whatever their individual effects, most alkaloids are toxic in large enough doses For some, the toxic dose is very small! ( S )-Coniine is the toxic principle of water hemlock (a member of the carrot family) Its ingestion can cause weakness, labored respiration, paralysis, and eventually death It was the toxic substance in the “poison hemlock” used in the death of Socrates Water hemlock is easily confused with Queen Anne’s lace, a type of wild carrot— a mistake that has killed numerous people (S)-Nicotine occurs in the tobacco plant In small doses, it is an addictive stimulant In larger doses, this substance causes depression, nausea, and vomiting In still larger doses, it is a deadly poison Solutions of nicotine in water are used as insecticides H H N N N CH2CH2CH3 CH3 Image not available due to copyright restrictions H (S)-Coniine H3C (S)-Nicotine O N COCH3 H OCC6H5 H Cocaine O Cocaine is a central nervous system stimulant obtained from the leaves of the coca plant In small doses, it decreases fatigue and gives a sense of well-being Prolonged use of cocaine leads to physical addiction and depression 444 ■ Chapter 16 Amines 16.2 How Do We Name Amines? A IUPAC Names IUPAC names for aliphatic amines are derived just as they are for alcohols The final -e of the parent alkane is dropped and replaced by -amine Indicate the location of the amino group on the parent chain by a number NH2 NH2 H2N CH3CHCH3 2-Propanamine Cyclohexanamine NH2 1,6-Hexanediamine IUPAC nomenclature retains the common name aniline for C6H5NH2, the simplest aromatic amine Its simple derivatives are named using numbers to locate substituents or, alternatively, using the locators ortho (o), meta (m), and para (p) Several derivatives of aniline have common names that remain in use Among them is toluidine for a methyl-substituted aniline NH2 NH2 NH2 CH3 NO2 Aniline 3-Methylaniline (m-Toluidine) 4-Nitroaniline ( p-Nitroaniline) Unsymmetrical secondary and tertiary amines are commonly named as N-substituted primary amines The largest group bonded to nitrogen is taken as the parent amine; the smaller groups bonded to nitrogen are named, and their locations are indicated by the prefix N (indicating that they are bonded to nitrogen) N NHCH3 N-Methylaniline CH3 CH3 N,N-Dimethylcyclopentanamine Example 16.2 IUPAC Names of Amines Write the IUPAC name for each amine Try to specify the configuration of the stereocenter in (c) (a) NH2 (b) H2N(CH2)5NH2 (c) H NH2 Strategy The parent chain is the longest chain that contains the amino group Number the parent chain from the end that gives the amino group the lowest possible number 16.2 How Do We Name Amines? Solution (a) The parent alkane has four carbon atoms and is butane The amino group is on carbon 2, giving the IUPAC name 2-butanamine (b) The parent chain has five carbon atoms and is pentane There are amino groups on carbons and 5, giving the IUPAC name 1,5-pentanediamine The common name of this diamine is cadaverine, which should give you a hint of where it occurs in nature and its odor Cadaverine, one of the end products of decaying flesh, is quite poisonous (c) The parent chain has three carbon atoms and is propane To have the lowest numbers possible, number the chain from the end that places the phenyl group on carbon and the amino group on carbon The priorities for determining R or S configuration are NH C 6H 5CH CH H This amine’s systematic name is (R)-1-phenyl-2-propanamine It is the (R)-enantiomer of the stimulant amphetamine Problem 16.2 Write a structural formula for each amine (a) 2-Methyl-1-propanamine (b) Cyclopentanamine (c) 1,4-Butanediamine B Common Names Common names for most aliphatic amines list the groups bonded to nitrogen in alphabetical order in one word ending in the suffix -amine NH2 NH2 N NH2 Propylamine sec-Butylamine Diethylmethylamine Cyclohexylamine Example 16.3 Common Names of Amines Write a structural formula for each amine (a) Isopropylamine (b) Cyclohexylmethylamine (c) Triethylamine Strategy and Solution In these common names, the names of the groups bonded to carbon are listed in alphabetical order followed by the suffix -amine (a) (CH3)2CHNH2 (b) NHCH3 (c) (CH3CH2)3N or or or H N NH2 Problem 16.3 Write a structural formula for each amine (a) 2-Aminoethanol (c) Diisopropylamine (b) Diphenylamine N ■ 445 ■ Chapter 16 Amines Charles D Winters/Cengage Learning 446 Several over-the-counter mouthwashes contain an N-alkylpyridinium chloride as an antibacterial agent d d d H (CH3CH2)3NHCl Triethylammonium chloride 16.3 What Are the Physical Properties of Amines? Like ammonia, low-molecular-weight amines have very sharp, penetrating odors Trimethylamine, for example, is the pungent principle in the smell of rotting fish Two other particularly pungent amines are 1,4-butanediamine (putrescine) and 1,5-pentanediamine (cadaverine) Amines are polar compounds because of the difference in electronegativity between nitrogen and hydrogen 3.0 2.1 0.9 Both primary and secondary amines have NiH bonds, and can form hydrogen bonds with one another (Figure 16.1) Tertiary amines not have a hydrogen bonded to nitrogen and, therefore, not form hydrogen bonds with one another An NiH>N hydrogen bond is weaker than an OiH>O hydrogen bond, because the difference in electronegativity between nitrogen and hydrogen 3.0 2.1 0.9 is less than that between oxygen and hydrogen 3.5 2.1 1.4 To see the effect of hydrogen bonding between alcohols Hydrogen bonding H d R NC R When four atoms or groups of atoms are bonded to a nitrogen atom—as, for example, in NH41 and CH3NH31—nitrogen bears a positive charge and is associated with an anion as a salt The compound is named as a salt of the corresponding amine The ending -amine (or aniline, pyridine, or the like) is replaced by -ammonium (or anilinium, pyridinium, or the like) and the name of the anion (chloride, acetate, and so on) is added R N R FIGURE 16.1 Hydrogen bonding between two molecules of a secondary amine Chemical Connections 16C Tranquilizers Most people face anxiety and stress at some time in their lives, and each person develops various ways to cope with these factors Perhaps this strategy involves meditation, or exercise, or psychotherapy, or drugs One modern coping technique is to use tranquilizers, drugs that provide relief from the symptoms of anxiety or tension The first modern tranquilizers were derivatives of a compound called benzodiazepine The first of these com- H N N N Benzodiazepine Cl pounds, chlorodiazepoxide, better known as Librium, was introduced in 1960 and was soon followed by more than two dozen related compounds Diazepam, better known as Valium, became one of the most widely used of these drugs Librium, Valium, and other benzodiazepines are central nervous system sedatives/hypnotics As sedatives, they diminish activity and excitement, thereby exerting a calming effect As hypnotics, they produce drowsiness and sleep CH3 NH CH3 N O Chlorodiazepoxide (Librium) O N N Cl Diazepam (Valium) 16.4 How Do We Describe the Basicity of Amines? and amines of comparable molecular weight, compare the boiling points of ethane, methanamine, and methanol Ethane is a nonpolar hydrocarbon, and the only attractive forces between its molecules are weak London dispersion forces (Section 5.7A) Both methanamine and methanol have polar molecules that interact in the pure liquid by hydrogen bonding Methanol has the highest boiling point of the three compounds, because the hydrogen bonding between its molecules is stronger than that between methanamine molecules Molecular weight (amu) Boiling point °C CH 3CH CH 3NH CH 3OH 30.1 288.6 31.1 26.3 32.0 65.0 All classes of amines form hydrogen bonds with water and are more soluble in water than are hydrocarbons of comparable molecular weight Most low-molecular-weight amines are completely soluble in water, but higher-molecular-weight amines are only moderately soluble in water or are insoluble 16.4 How Do We Describe the Basicity of Amines? Like ammonia, amines are weak bases, and aqueous solutions of amines are basic The following acid–base reaction between an amine and water is written using curved arrows to emphasize that, in this proton-transfer reaction (Section 8.1), the unshared pair of electrons on nitrogen forms a new covalent bond with hydrogen and displaces a hydroxide ion H CH3 N H H9O9H H Methylamine (a base) CH3 N 9 H O9H H Methylammonium hydroxide The base dissociation constant, Kb, for the reaction of an amine with water has the following form, illustrated here for the reaction of methylamine with water to give methylammonium hydroxide pKb is defined as the negative logarithm of Kb Kb CH3NH31 OH2 4.37 1024 CH3NH2 pKb 2log 4.37 1024 3.360 All aliphatic amines have approximately the same base strength, pKb 3.0 4.0, and are slightly stronger bases than ammonia (Table 16.1) Aromatic amines and heterocyclic aromatic amines pKb 8.5 9.5 are considerably weaker bases than aliphatic amines One additional point about the basicities of amines: While aliphatic amines are weak bases by comparison with inorganic bases such as NaOH, they are strong bases among organic compounds ■ 447 448 ■ Chapter 16 Amines TABLE 16.1 Approximate Base Strengths of Amines Class pK b Aliphatic 3.024.0 Ammonia 4.74 Aromatic 8.529.5 Example Name CH 3CH 2NH Ethanamine Stronger base Aniline Weaker base NH2 Given the basicities of amines, we can determine which form of an amine exists in body fluids—say, blood In a normal, healthy person, the pH of blood is approximately 7.40, which is slightly basic If an aliphatic amine is dissolved in blood, it is present predominantly as its protonated or conjugate acid form NH2 HO HO HO NH3 HO Dopamine Conjugate acid of dopamine (the major form present in blood plasma) We can show that an aliphatic amine such as dopamine dissolved in blood is present largely as its protonated or conjugate acid form in the following way Assume that the amine, RNH2, has a pKb of 3.50 and that it is dissolved in blood, pH 7.40 We first write the base dissociation constant for the amine and then solve for the ratio of RNH31 to RNH2 RNH2 H2O m RNH31 OH2 Kb RNH31 OH2 RNH2 RNH31 Kb OH2 RNH2 We now substitute the appropriate values for Kb and OH2 in this equation Taking the antilog of 3.50 gives a Kb of 3.2 1024 Calculating the concentration of hydroxide requires two steps First recall from Section 8.8 that pH pOH 14 If the pH of blood is 7.40, then its pOH is 6.60 and its OH2 is 2.5 1027 Substituting these values in the appropriate equation gives a ratio of 1300 parts RNH31 to part RNH2 RNH31 3.2 1024 5 1300 RNH2 2.5 1027 As this calculation demonstrates, an aliphatic amine present in blood is more than 99.9% in the protonated form Thus, even though we may write the structural formula for dopamine as the free amine, it is present in blood as the protonated form It is important to realize, however, that the amine and ammonium ion forms are always in equilibrium, so some of the unprotonated form is nevertheless present in solution 16.5 What Are the Characteristic Reactions of Amines? Aromatic amines, by contrast, are considerably weaker bases than aliphatic amines and are present in blood largely in the unprotonated form Performing the same type of calculation for an aromatic amine, ArNH2, with pKb of approximately 10, we find that the aromatic amine is more than 99.0% in its unprotonated (ArNH2) form Example 16.4 Basicity of Amines Select the stronger base in each pair of amines NH2 CH3 O (a) (b) or N CH2NH2 or N (C) (D) H (A) (B) Strategy Determine whether the amine is an aromatic or an aliphatic amine Aliphatic amines are stronger bases than aromatic amines Solution (a) Morpholine (B), a 2° aliphatic amine, is the stronger base Pyridine (A), a heterocyclic aromatic amine, is the weaker base (b) Benzylamine (D), a 1° aliphatic amine, is the stronger base Even though it contains an aromatic ring, it is not an aromatic amine because the amine nitrogen is not bonded to the aromatic ring o-Toluidine (C), a 1° aromatic amine, is the weaker base Problem 16.4 Select the stronger base from each pair of amines N (a) or NH2 (A) (b) CH3NH2 (B) or NH2 (C) (D) 16.5 What Are the Characteristic Reactions of Amines? The most important chemical property of amines is their basicity Amines, whether soluble or insoluble in water, react quantitatively with strong acids to form water-soluble salts, as illustrated by the reaction of (R)-norepinephrine (noradrenaline) with aqueous HCl to form a hydrochloride salt HO H HO H HO NH2 HO HCl HO (R)-Norepinephrine (only slightly soluble in water) NH3 Cl H2O HO (R)-Norepinephrine hydrochloride (a water-soluble salt) ■ 449 450 ■ Chapter 16 Amines Chemical Connections 16D The Solubility of Drugs in Body Fluids O Many drugs have “•HCl” or some other acid as part of their chemical formula and occasionally as part of their generic name Invariably these drugs are amines that are insoluble in aqueous body fluids such as blood plasma and cerebrospinal fluid For the administered drug to be absorbed and carried by body fluids, it must be treated with an acid to form a water-soluble ammonium salt Methadone, a narcotic analgesic, is marketed as its watersoluble hydrochloride salt Novocain, one of the first local anesthetics, is the hydrochloride salt of procaine N CH3 ·HCl H3C Methadone ·HCl O N O • HCl H 2N Beverly March Procaine ·HCl (Novocain, a local anesthetic) These two drugs are amino salts and are labeled as hydrochlorides There is another reason besides increased water solubility for preparing these and other amine drugs as salts Amines are very susceptible to oxidation and decomposition by atmospheric oxygen, with a corresponding loss of biological activity By comparison, their amine salts are far less susceptible to oxidation; they retain their effectiveness for a much longer time Example 16.5 Basicity of Amines Complete the equation for each acid–base reaction, and name the salt formed (a) (CH3CH2)2NH HCl (b) CH3COOH N Strategy Each acid–base reaction involves a proton transfer from the acid to the amino group (a base) The product is named as an ammonium salt Solution (CH3CH2)2NH2Cl (a) Diethylammonium chloride CH3COO (b) N H Pyridinium acetate Problem 16.5 Complete the equation for each acid–base reaction and name the salt formed (a) (CH CH ) N HCl 3 (b) NH CH3COOH Index Fischer esterification of carboxylic acids, 488–90, 493, 501, 513 Fischer projections, 518, 518–19, 539 formulas, 518–19 Fleming, Alexander, 501b Florey, Howard, 501b Fluid mosaic model of membranes, 552, 553 Fluoride in drinking water, 71 Fluorine, 44 electronegativity of, 74 Fluorouracil, 670b Food See also Diet, human body processing of, 792–94 counting calories in, 791–92 nutrition in See Nutrients; Nutrition, human performance-enhancing, 803b Food additives, 489b Food dyes, 391b Food Guide Pyramid, 789, 790b Food labels, 788 Food metabolism See Catabolism Formaldehyde (CH2O), 460 Lewis structure and ball-and-stick model of, 83 molecular shape of, 94 reaction between hydrogen and, to produce methanol, 221 Formic acid, 460, 476 Formula, 33, 34 line-angle, 324 predicting, for ionic compounds, 76–77 structural, 83 See also Structural formulas Formula weight (FW), 109, 109–10, 133 for two ionic, and two covalent compounds, 109t Franklin, Rosalind (1920–1958), 672, 673 Free radicals, 293b Freezing-point depression, 197–98, 204 Freons, 345, 345b Frequency (n), electromagnetic radiation, 278 Fructofuranose, 525 Fructose catabolism and, 754 cyclic hemiacetals of, 525 D- form of, 519, 520t Fructose 1,6-bisphosphate, 749, 750 Fruits, ethylene and ripening of, 353b FTO, 779b Fuller, Buckminster (1895–1983), 164 Fumarate, 735, 763 Functional groups, 313–18 alcohols, 313, 313–14, 398 aldehydes and ketones, 316, 316–17 amines/amino groups, 315, 315–16 carboxylic acids, 317, 317–18 carboxylic esters, 318 common types of, 313t defined, 313, 319 ethers, 408 thiols, 411, 412 Fungus (fungi), growth inhibitors of, 486 -furan-, 523 Furanose, 523, 539 Furchgott, Robert, 654b Fusion, nuclear, 296, 296–97 G GABA (g -Aminobutyric acid), 477, 649 gag gene, 831 Galactosamine, 521 Galactose catabolism and, 754 D- form of, 519, 520t, 532b inability to metabolize, 522b Galactosemia, 522b Galantamine, 648b Galen (200–130 BCE), Gallstones, 561 Gamma emission, 283, 301 Gamma (g) rays, 278, 278–79, 301 Gangliosides, 556 Gap junctions, 554b Gaseous state, 142 Gas(es), 17, 26, 142 Avogadro’s law, idea gas law and, 148–50 Boyle’s law, Charles’s law, and Gay-Lussac’s law governing behavior of, 144–48 condensation of, 153 Dalton’s law of partial pressure and, 150–52 Henry’s law and solubility of, 182–83 ideal, 148 kinetic molecular theory on behavior of, 152–53, 219 noble, 48, 49t phase change from solid to, 166–70 pressure and reaction rates between, 217 pressure change and chemical equilibrium between, 233–35 solubility of select, in water, 180t Gasoline, octane rating of, 343b Gaucher’s disease, 559t Gauze, 537b Gay-Lussac’s law, 146, 146t, 170 GC box, 710 Geiger-Müller counter, 287, 301 Gene(s), 666, 679, 691 See also Human Genome Project coding and noncoding sequences in (exons, introns), 679, 680, 698, 698 CYP2D6, and drug metabolism, 687b mutations in, 291, 715–17, 820 structural, 697, 698 transcription of See Transcription Gene conversion (GC) mutation, 820 Gene expression, 696, 696–725 defined, 696 DNA manipulation and, 718–20 DNA transcription into RNA, 697–99 gene regulation and, 708–14 genetic code and, 700–702 mutations, 715–17 proteins’ role in, 579 stages of protein synthesis as, 702–8 translation and protein synthesis facilitated by RNA in, 700 General transcription factor (GTF), 710 Gene regulation, 708–14 of post-transcriptional level, 713, 714 on transcriptional level, 710–12 on translational level, 714 Gene therapy, 686b, 721–22 Genetic code, 700, 701t, 723 second, 703 Genomics, 602b personal, 685b response to drugs based on individual, 687b Geometries of carbon compounds, 311t Geraniol (rose, other flowers), 362 Geranyl pyrophosphate, 781 GILT (gamma-interferon inducible lysosomal thiol reductase), 816 Globin gene, exons and introns of, 679 Globular proteins, 579 Glucagon, 656 Glucocerebrosides, 559b Glucocorticoids, 829 Glucogenic amino acids, 764, 768 Gluconate, 529 Gluconeogenesis, 774, 784 Glucophage (Metformin), 659b Glucopyranose, 528, 529, 534 chair conformations of, 525 b-D-glucopyranose, 528 ■ I10 Haworth projections of, 523, 524 mutarotation of, 527, 540 Glucosamine, 521 Glucose (C6H12O6), 518 blood levels of, 518, 520, 530b, 659b, 792 breakdown of glycogen to, 630b, 748–49, 755 carbohydrate conversion of, 775–77 catabolism of, 748–53 CO2 conversion to, in plants, 773, 775b–776b D- form of, 519, 520t glycolysis of, 748–53 ketone bodies formed in response to shortages of, 758–59 medical imaging of uptake and metabolism of, 294 oxidation of, enzymes and, 615 reaction rate of, with oxygen, 211 reduction of D-, to D-sorbitol, 528 synthesis of, 774–75 Glucose oxidase, 527 Glucose 6-phosphate, 748, 752 Glucuronic acid, 531, 538 Glutamate, 585, 764 biosynthesis (anabolism) of amino acids and, 782, 783 oxidative deamination of, 761, 761–62, 764 transamination and formation of, 761 Glutamic acid, 581, 585 drugs affecting messenger function of, 641t reuptake of, 649 Glutamine, 581, 764 Glutathione protection against oxidative damage and role of, 753 Glyceraldehyde, 518 amino acid configuration in, 580, 583 enzyme surface and interaction with R and S, 436 stereocenter and enantiomers of, 518, 519 Glyceraldehyde 3-phosphate, 749, 755 Glycerin, 400, 401b, 414 Glycerol, 400, 547, 748, 780 catabolism of, 755 Glycerol 1-phosphate, 780 Glycerol 3-phosphate, 753 Glycerophospholipids, 551, 553–55, 573 Glycine, 581, 583, 594 Glycocholate, 569 Glycogen, 536, 540 breakdown of, to form glucose, 630b, 748–49, 755 depletion of, in athletes, 803b enzyme actions on, 792 role of glycogen phosphorylase in breakdown or synthesis of, 630b, 757b, 773 Glycogenesis, 777 Glycogenolysis, 754 Glycogen phosphorylase, 627 effects of signal transduction on, 757b as enzyme regulation model, 630b Glycogen synthase, 757b Glycol, 400, 414 Glycolic acid, 512b Glycolipids, 551, 556–57, 573, 780 Glycolysis, 622b, 748–53, 768 citric acid cycle and, 752 energy yield from glucose catabolism, 753–55 of glucose, 748–51, 750, 751, 752 glycerol catabolism and, 755 overview, and entrances/exits from, 751 pentose phosphate pathway and, 752–53, 753 phosphoric esters in, 509 pyruvate as end product of, 465 Glycoproteins cytokines as, 824 immunoglobulins as, 816 I11 ■ Index Glycosides (acetals), formation of, 527, 527–28, 540–41 Glycosidic bonds, 527, 534, 536, 538 in DNA and RNA nucleosides, 667–68, 668 hydrolysis of, which link monosaccharides, 792 Goldstein, Joseph, 561 Golgi bodies, 729 Gonorrhea, drug resistant strains of, 828b Good, N E., 267 Gout, 192, 193 G-protein, 650 cascade of adenylate cyclase and, 650, 651, 652 effect of cholera toxin on, 652 Gram (g), defined, 10 Graphite, surface of, 42 Gravity, 10–11 specific, 19, 19–20 Ground-state electron, 49 configurations for, of first 18 elements, 53t GTP See Guanosine triphosphate (GTP) Guanine (G), 666, 667, 668, 672, 673 Guanosine, 668 Guanosine diphosphate (GDP), 650, 651 Guanosine triphosphate (GTP) formation of, in citric acid cycle, 735 signal transduction cascade and, 650, 651 Guillain-Barré syndrome, 558b H Haber process, 234b Hahn, Otto (1879–1968), 298 Hair, reversible denaturation of proteins in, 607–8 Half-life t1/2, 284–86, 300 radioactive dating of archeological objects based on, 285b of select radioactive nuclei, 286t Haloalkanes, 344–45 chlorofluorocarbons, 344–45 as solvents, 345 Halogenation of alkanes, 343–44, 346, 368–69, 375 of benzene and derivatives, 387, 394 Halogens, 44, 44 alkane reactions with, 343–44, 346 melting and boiling points of, 48t Harvey, William (1578–1657), 4–5 Haworth, Walter N., 523 Haworth projection, 523, 523–25, 540 Heart, human angina, 401b, 624b atherosclerosis and, 561, 563 conversion of lactate to pyruvate in, 628 lactate accumulation in, 752b myocardial infarction in, 563, 629 Heat, 20–25, 26 measurement of, 21–22 produced by chemical reactions, 133 specific See Specific heat (SH) temperature and, 21–22 Heat energy, 20 conversion of chemical energy to, 742 Heating curve for phase change from ice to water vapor, 166, 166, 167 Heat of combustion, 134 Heat of fusion, 166, 171 Heat of reaction, 133, 133 Heat of vaporization, 166, 171 Helicases, 686, 691, 697 Helicobacter pylori bacterium, 655 Helium (He), orbital box diagram for, 52 a-Helix, protein secondary structure, 596, 609 Helix-turn-helix transcription factor, 712 Helper T cells (TH cells), 814 development of, 815 HIV infection and, 824, 830 Heme protein as coenzyme, 618 in myoglobin and hemoglobin, 606b reactions of catabolizing, 766–67 structure of, 604 Hemiacetal, 465, 465–66 formation of monosaccharide cyclic, 522–27, 540 Hemodialysis, 203b Hemoglobin, 579, 592, 601 amino-acid sequence of N-terminal decapeptides of b-globins, in select species, 715b comparison of, with myoglobin, 606b sickle cell disease and, 595, 596b, 679, 716 structure of, 601, 604 transport of oxygen by, 606b Hemolysis, 202, 204 Henderson-Hasselbalch equation, 265, 265–67 Henry’s law, 182, 183 Heparin, 539, 539 HEPES buffer, 269t Heptane, 343b Herbicides, 191 Herceptin (drug), 821b Heredity, 665–94 DNA amplification, 689–91 DNA repair, 687–89 DNA replication, 679–86 DNA structure, 666, 670–76 genes, 666, 679 information flow in, 676 molecules of, 665–66 nucleic acid structure and, 666–69 RNA, 666, 670–78 Heroin, 632b Herpes virus, 709b Heterocyclic aliphatic amine, 442 Heterocyclic amine, 442, 452 Heterocyclic aromatic amine, 442 Heterogeneous catalyst, 220 Hexanal, 462 Hexanediamine (hexamethylenediamine), 510 1,6-Hexanediamine (hexamethylenediamine), 444 Hexanedioic acid (adipic acid), 476, 510 Hexanoic acid (caproic acid), 462, 476 Hexanol, 458 Hexene, 355, 357 High-density lipoproteins (HDL), 481b, 561, 573 blood serum levels of, 563 composition and properties of human, 562t transport of cholesterol by, 562–63 High-density polyethylene (HDPE), 372–73, 373 Highly active antiretroviral therapy (HAART), 832 Histamine, 654–55 drugs affecting messenger function of, 641t Histidine, 582, 585, 623, 625, 654 Histone(s), 666, 673, 675, 691 acetylation and deacetylation of key, 683 Histone deacetylase, 683 HIV See Human immunodeficiency virus (HIV) HIV-1 protease, 614, 624b HMG-CoA reductase, 563 Homogeneous catalyst, 220 Homogeneous mixture, 179 See also Solution(s) Homosalate, 506b Hormones chemical messenger functions of, 640, 641–43, 661 pituitary, 643 principal, 642t proteins as, 579 sex hormones, 565–68 steroid See Steroid hormones Hot-air balloons, 146 Household substances, 257 Human body anesthesia and effect of ethers on, 410b blood See Blood, human blood pressure, 159b bone grafts, 73b brain See Brain, human breath-alcohol screening, 407b breathing, and Boyle’s law on gases, 145b calcium in, and strontium-90 hazards to, 45b cis-trans isomerism in human vision, 361b diet See Diet, human diseases and conditions affecting See Diseases and conditions drugs and See Drugs drug solubility in, 450b electrolyte maintenance, sports drinks for, 194 elements in, 37b elements required by, 33b eye, and vision See Eye, human fever, 219b goiter, and iodide ion, 388b gout caused by sodium urate monohydrate in joints of, 192, 193 heart See Heart, human hypothermia/hyperthermia in, 22b immune system See Immune system; Immunity kidneys, 203b lowering temperature of, 221b mass of, and drug dosage, 11b medical care of See Medicine muscles See Muscle(s) nuclear radiation effects on, 286, 289–91 nutrition See Nutrition, human obesity, 481b, 738b oral contraception for, 568b pH of fluids in, 257 poisons that affect, 337b polynuclear aromatics effects on, 387b radon effects on, 292b smoking effects on, 387b sun protection for, 506b tissue damage caused by radiation free radicals, 293b tooth decay, 127b toxins that affect or toxins affecting, 337b water in, 195 Human Genome Project, 602b, 685b–686b, 713 Human immunodeficiency virus (HIV), 829–36 CD4 molecule, helper T cells and, 824, 830 infection process, 830 methods of attacking immune system, 832 search for vaccine against, 832, 833, 833 structure of, 830 treatment for infection by, 614, 624b, 832 Hyaluronic acid, 538 Hybridization of nucleic acids, 689 Hybridoma, 822 Hydrated ions, 191 Hydrates, 191 air pollution caused by, 194b Hydration, 366 acid-catalyzed, 366–68, 375 alkenes reactions of, 363t, 366–68 Hydrocarbons, 323, 346 aliphatic, 324 alkanes, 324 See also Alkanes alkenes, 324 See also Alkenes alkynes, 324 See also Alkynes arenes, 324 See also Benzene (C6H6) cyclic, 332 See also Cycloalkane(s) saturated, 324 thermal cracking of, 353 unsaturated, 324 Hydrochloric acid (HCl), 243b addition of, to 2-butene, to alkenes, 365 hydrolysis of proteins by, 748 Index magnesium and, reaction between, 251 methylamine and, reaction between, 253 norepinephrine and, reaction between, 449 polar covalent bond, 80, 81 potassium hydroxide and, reaction between, 251 reaction between bicarbonate ion and, to form carbon dioxide, 125 reaction between water and, 214, 241, 247 solubility in water, 195 in stomach acid, 794 See also Stomach acid Hydrochlorination reactions in alkenes, 363t, 363–66 Hydrochlorofluorocarbons (HCFCs), 345b Hydrofluorocarbons (HFCs), 345b a-Hydrogen, 468 Hydrogenation in alkenes, 363t, 369–70, 376 catalytic, 369 of lipids, 549–50 Hydrogen bond(s), 79, 153t, 155, 155–56, 171 intermolecular, 597 intramolecular, 597 nucleic acid base pairs and, 673 Hydrogen bonding, 401, 414 between secondary amine molecules, 446 tertiary protein structure stabilized by, 599, 609 Hydrogen cyanide, structural formula, 311t Hydrogen (H) addition of, to alkenes, 369–70 covalent bonds, 79–80 electron configuration in, 49 orbital box diagram of, 52 reaction between formaldehyde and, to produce methanol, 221 transport of H1, 731, 737–39, 741 Hydrogen halides, addition of, to alkenes, 363–66 Hydrogen sulfide, 87 Hydrohalogenation, 363–66 Hydrolases, 616, 617t Hydrolysis, 503–7 acetals, 467 amides, 505 anhydrides, 503 esters, 503–4 glycosidic bonds, 792 triglycerides, 550b Hydrometer, 20 Hydronium ion, 195, 241 expressed as pH and pOH, 256–58 Hydroperoxides, 393 Hydrophobic interactions, tertiary protein structure stabilized by, 598, 599, 609 Hydroxides, 127t Hydroxy-, 460, 476 3-Hydroxybutanoic acid, 492b b-Hydroxybutyrate as component of ketone bodies, 759 5-Hydroxyhexanoic acid, 476 Hydroxyl group, 314, 319, 414 alcohol and, 398 monosaccharides and, 522 phenols and, 389 Hydroxylysine, 586, 587 4-Hydroxy-3-methoxybenzaldehyde (vanillin), 390 4-Hydroxymethylcyclopentene, 488 Hydroxymethylglutaryl CoA, 781 4-Hydroxypentanal, 522 Hydroxyproline, 586, 587 2-Hydroxypropanoic acid See Lactic acid Hydroxyurea, 596b Hygroscopic substance, 192 Hyperbaric chamber, 151b Hyperbolic curve, 606b Hyperglycemia, 530b Hypertension, 624b Hyperthermia, 22b Hypertonic solutions, 202, 204 Hyperventilation, 269b Hypoglycemia awareness, 595b Hypothalamus, 655 Hypothermia, 22b Hypothesis, 3, 26 Hypotonic solutions, 202, 204 Hypoxia, 151b I Ibuprofen, 311, 502b, 572 enantiomerism in, 427, 437 -ic acid (suffix), 499 Ice density of water and, 162b phase change from, to water vapor, 166–70 Ideal gas, 148, 153 Ideal gas constant, 148 Ideal gas law, 148 -ide (suffix), 528 Ignaro, Louis, 654b Immune response See also Immune system regulation of, 824, 826 speed of, 811–12 Immune system, 809–39 adaptive immunity and, 810, 810–11 antigen simulation of, 815 cells of, 812–15, 813t components of, 811 HIV, AIDS, and, 829–36 immunoglobulins, 816–22 introduction to, 809–12 organs of, 812–15 overview, 810 proteins’ role in, 579 regulation of, 824, 826 self versus nonself, determination by, 826–29 specificity, and memory of, as key features, 810–11 T cells and T-cell receptors of, 822–24 Immunity, 809 adaptive, 810, 810–11 innate, 810, 814 vaccinations and, 825b Immunizations, 825b Immunogen, 630 Immunoglobulin(s), 811, 816, 836, 836 See also Antibodies; Major histocompatibility complexes (MHC); T-cell receptor(s) B cell synthesis of, and function, 818, 819 classes of, 816–17, 817t constant, and variable domains on molecules of, 811, 836 IgA, 817 IgE, 818 IgG, 816, 818 IgM, 816 monoclonal antibodies and, 822 structure, 817–18 T-cell receptors and, differences between, 823 V(J)D gene and diversification of responses in, 819, 820, 820 Imprinting, genetic information, 835b Indomethacin, 572 Induced-fit model of enzyme activity, 620, 620–23, 634 Inflammatory response, 824 Influenza virus, 709b Infrared light, 278 Inhibition, enzyme, 618, 620, 621, 623, 633 medical uses of, 624b Inhibitory neurotransmitters, 649 Inhibitory receptor, 827, 837 Initial rate of reaction, 211, 218 ■ I12 Initiation factors, 703, 704 Initiation signal, 698 Initiation stage of protein synthesis, 703, 704 Innate immunity, 810, 836 cells of, 814 self/nonself discriminate in cells of, 826–27 Inner transition elements, 44 Inorganic compounds, 309t Insect pests, corn borers as, 358b Insulin, 656–57, 665 A and B chains of, 594 diabetes and production of, 530b, 659b polypeptide structure of, 594 production of, by recombinant DNA techniques, 719 use of, 595b Integral membrane proteins, 604 Intensity of ionizing radiation, 287–88 Interleukins (ILs), 824 Intermolecular forces See Attractive forces between molecules Intermolecular hydrogen bonds, 597 International System of Units (SI), International Union of Pure and Applied Chemistry (IUPAC), 328–29, 346 See also IUPAC naming system Intramolecular hydrogen bonds, 597 Introns, 679, 680, 691, 698, 698 In vivo gene therapy, 721–22, 723 Iodide, reaction between chloromethane and, 216 Iodine, 44 Iodine-125, 296 Iodine-131, 293, 296 decay curve of, 284 Ion(s), 59, 61 See also Anion; Cation electricity conducted by solutions of, 192–93 forces of attraction between molecules and, 153t, 153–56 hydrated, 191 naming polyatomic, 72 predicting reactivity of, in aqueous solutions, 124–27 spectator, 125 Ion channel, chemical messengers and opening of, 646, 648, 651 Ionic bonds, 68, 73–74, 74, 75–77, 100, 153t formation of, 75–76 Ionic compound(s), 75 containing polyatomic ions, 79 formula weights for two, 109t in medicinal drugs, 80b from metals forming more than one positive ion, 78–79 from metals forming one positive ion, 77–78 molar mass as conversion factor for, 111 predicting formulas of, 76–77 water as solvent of, 191, 192 Ionization energy, 59, 60, 61 atomic number versus, 60 Ionization of water, 254 Ionizing radiation, 286–89 energy of, 288–89 intensity of, 286–89 as mutagens, 716 b-Ionone, 461b Ion product of Kw (water constant), 254, 270 Iron daily requirements for, 798b in food, 798b mixture of sulfur and, 35 Isobutane, 331 Isobutylene, 356 Isocitrate, oxidation and, decarboxylation of, 734–35 Isoelectric point (pI), 584, 591–92, 592, 608 Isoleucine, 582 I13 ■ Index Isomer(s), 421 constitutional, 326–28 stereoisomers, 339 See also Stereoisomers Isomerases, 616, 617t Isopentane, 331 Isopentenyl pyrophosphate, 781 Iso- (prefix), 331 Isoprene, 359, 362, 781 Isoprene unit, 362, 375 Isopropyl alcohol, 414 2-Isopropyl-5-methylcyclohexanol, 433 2-Isopropyl-5-methylphenol (Thymol), 390 Isoproterenol, 451b Isotonic solutions, 201 Isotopes, 40–41, 61 radioactive, 279–80, 294t Isotopic abundance, 43b Isozymes (isoenzymes), 628, 628, 634 -itol (suffix), 528 IUPAC naming system, 328–29, 346 alcohols, 398–400 aldehydes and ketones, 458–61 alkanes, 328–31 alkenes and alkynes, 355–56 amines, 444–45 carboxylic acids, 475–76 prefixes used in, to show carbon presence, 329t J Jackson, Charles, 410b Jencks, William, 630 Jenner, Edward, 825b Joule (J), 22 K Ka, acid ionization constant, 249, 270 for weak acids, 249t Kekulé, August (1829–1896), 308 Kekulé’s structure of benzene, 383 Kelvin (K) temperature scale, 12, 143b gas laws and, 146 Keratin, 579, 597, 607 a-Ketoacid, 761 Ketoacidosis, 760b b-Ketocarboxylic acid, decarboxylation of, 491 Keto-enol tautomerism, 468–69, 470, 491 Ketogenic amino acids, 765, 768 a-Ketoglutarate, 491, 735, 761, 782, 783 a-Ketoglutaric acid, 491, 765 Keto group, 761 2-Ketohexoses, D-forms of, 521t Ketone(s), 457–74, 458 characteristic reactions of, 462–68 functional group, 313t, 316, 316–17, 458 keto-enol tautomerism, 468–69 naming, 458–61 naturally occurring, 461b oxidation of secondary alcohol to, 406, 415 physical properties of, 461–62 Ketone bodies, 758–59, 759, 765, 768, 794 diabetes and, 492b, 760b 2-Ketopentoses, D-forms, 521t Ketoses, 518 as reducing sugars, 529 Ketosis, 794 Kevlar, 510 Kidneys, hemodialysis of human, 203b, 204 Killer (cytotoxic) T cells (Tc cells), 814 Kinases, 621b Kinetic energy (KE), 20, 26 conversion of potential energy to, 20 temperature and increase in, 142, 219 Kinetic molecular theory, 152, 152–53, 171 chemical reactions and, 213–14, 219 Knoop, Franz, 755 Köhler, Georges, 822 Koshland, Daniel, 620 Krabbe’s leukodystrophy, 559t Krebs, Hans (1900–1981), 734, 764 Krebs cycle See Citric acid cycle Kwashiorkor, 782b, 795 L Laboratory tools See Tools Lactams, 500 b-lactam antibiotics, 501b b-Lactams, 501b Lactate accumulation of, in muscles, 752b glucose conversion of, 774, 774 glycolysis, glucose catabolism, and, 750, 751, 752 pyruvate conversion of, 628 Lactate dehydrogenase (LDH), 629 isozymes of, 628, 628 Lactic acid, 479, 510 muscle tissue and production of, 435 rotations for enantiomers of, 435 Lactones, 499 Lactose, 534, 540 Lagging strand, DNA replication, 681, 682, 691 Lakes, specific heat of water and temperature of, 23b Landsteiner, Karl (1868–1943), 532b Laser surgery, human eye, 607b Lavoisier, Antoine Laurent (1743–1794), 36 Law of conservation of energy, 21 Law of conservation of mass, 36, 60, 114 Law of constant composition, 36, 60 L-dopa (L-Dihydroxyphenylalanine), 586, 653b Lead, 36, 43 Leading strand, DNA replication, 681, 682, 691 Le Chatelier, Henri (1850–1936), 229 Le Chatelier’s principle, chemical reactions and, 229, 229–35, 235 addition of reaction component and, 229–31 change in pressure and, 233–35 change in temperature and, 232–33 effects of catalyst and, 235 overcoming effects of, in biosynthetic pathways, 773 removal of reaction component in, 231–32 sunglasses and application of, 233b Lecithin, 553 Length, measurement of, 8–9 Leptin, 656 Lerner, Richard, 630 Leucine, 581, 701, 765 Leucine zipper, 712 Leukocytes See White blood cells (leukocytes) Leukotriene receptors (LTRs), 572 Leukotrienes, 572, 573 Levorotatory rotation, 435, 437 Lewis, Gilbert N (1875–1946), 55, 69 Lewis dot structures, 55–56, 61, 83, 100 for alkali metals, 57t for covalent compounds, 82–86 for elements 1-18, 55t for select small molecules, 84t Ligand-gated ion channels, 648 Ligands See Chemical messengers Ligases, 616, 617t Ligation process in DNA replication, 686 Light as energy, 20 IR (infrared), 278 plane-polarized, 434–35 reaction between silver chloride on sunglasses and sun, 233b Tyndall effect of colloid-sized particles on, 195–96 UV (ultraviolet), 278 visible, 278 Light reactions, photosynthesis, 775b–776b Limiting reagent, 121, 121–22, 134 Limonene, 362 Line-angle formula, 324 Linear alkylbenzenesulfonates (LAS), 484 Linoleic acid, 549, 553, 794 Linolenic acid, 794 Lipases, 615, 748, 794 Lipid(s), 546–77, 572 cell membrane transport, 554b classification of, 546–47 complex, 551, 551 function-based classification of, 546–47 glycerophospholipids, 553–55 glycolipids, 556–57 membrane structure and role of, 552–53 metabolism of See Lipid catabolism myelin sheath around nerve axons and, 558b oxidation and rancidity of, 550b processing of, 794 prostaglandins, thromboxanes, and leukotrienes, 569–72 simple, 551 sphingolipids, 555, 555–56 steroids, 558, 558–63 See also Steroid(s) storage disease of, in humans, 559b–560b structure-based classification of, 547 triglycerides, 547–51 waxes, 550b Lipid bilayers, 552, 573 space-filling molecular model of, 553 transport across, 554b Lipid biosynthesis, 777–80 Lipid catabolism, 733, 748 energy yield from, 757–58, 758t glycerol catabolism, 755 b-oxidation of fatty acids, 755–57 Lipoproteins, 561 cholesterol transport by, 561–63 composition and properties of human, 562t high-density (HDL) See High-density lipoproteins (HDL) low-density See Low-density lipoproteins (LDL) Liquid(s), 17, 26, 142 behavior of, at molecular level, 157–63 boiling point of, 161–63 density of water versus ice, 162b solidification of, 153 surface tension on, 158 vapor pressure of, 158–61, 161 Liquid state, 142 Liter (L), defined, Lithium aluminum hydride (LiAlH4), 488, 493 Lithium (drug), 71 Lithium (Li), orbital box diagram for, 52 Lock-and-key model of enzyme activity, 620, 634 Logarithms (logs), using antilogs and, 255–56 London, Fritz (1900–1954), 154 London dispersion forces, 153t, 154, 171 Low-density lipoproteins (LDL), 481b, 561, 573, 780 blood serum levels of, 563 composition and properties of human, 562t structure of, 562 transport of cholesterol in, 561–62 Low-density polyethylene (LDPE), 372 fabrication of, 372 Lowry, Thomas, 244, 270 Luteinizing hormone (LH), 565 Lyases, 616, 617t Lymph, 812, 813 Lymphatic system, 813, 814–15, 836 Lymph nodes, 813, 814–15 Lymphocytes, 812, 836 See also B cell(s); T cell(s) development of, 815 effect of vaccines on, 825b monoclonal antibody production from, 822 Lymphoid organs, 812, 836 Lysine, 582, 586, 615 Index Lysosomes, 615, 729 antigen processing in, 816 Lysozyme, 615 M Macrolide drugs, 829 Macrophages, 810, 812, 814, 815, 836 self/nonself determination and, 826–27 Mad cow disease, 600b Magnesium hydroxide (Mg(OH)2), 243b Magnesium metal, reaction with hydrochloric acid, 251 Main-group elements, 44 atomic radii of, 57, 59 Major groove, B-DNA, 674 Major histocompatibility complexes (MHC), 811, 814, 815–16 classes of (MHC I, MHC II), 815–16, 816 Malate, 736 Maloney murine leukemia virus (MMLV), 721, 722 Malonyl-CoA, 779b Malpighi, Marcelo (1628–1694), Maltose, 534, 540 Mannitol, 529 Mannosamine, 521 Manometer, mercury, 144, 144 MAO inhibitors, 652 Marasmus, 791 Markovnikov, Vladimir (1838–1904), 364 Markovnikov’s rule, 364, 366 Mass defined, 10 law of conservation of, 36, 61, 114 measurement of, 10–11 Mass number, 39, 61 Mass per unit volume See Density Mass relationship calculations chemical reactions, 118–24 using moles, 110–14 Matrix, mitochondria, 729 Matter, 1–3 atoms as basic component of, 31–32 classification of, 32–35 See also Compound(s); Element(s); Mixture(s) defined, energies involved in phase changes in, 166–70 states of, 2, 17–18, 141–42 See also Gas(es); Liquid(s); Solid(s) Mayapple (Podophyllum peltatum), antitumor effects of extract from, 817b MDR1, 716b Measurement, 8–12 of blood pressure, 159b of chemical reaction rates, 210–13 converting units of, 12–17 of energy dispersal (entropy), 143b of nuclear radiation, 286–89 of pressure, 143–44 Mechanical energy, 20 chemical energy conversion to, 742 Medical imaging, 292–95 positron emission tomography (PET), 295 radioactive isotopes useful for, 294t Medications See Pharmaceutical drugs Medicine, 1–2 See also Drugs; Human body; Pharmaceutical drugs anesthesia, 410b bone grafts, 73b dissolving surgical sutures, 512b enzymes and enzyme inhibition used in, 624b, 628–29 gene therapy, 721–22 hyperbaric oxygen chamber, 151b medical imaging of See Medical imaging nuclear, 292–96 Meitner, Lise (1878–1968), 298 Melting point, 142, 171 of alkali metals, 48t of alkanes, 340, 340t of halogens, 48t of noble gases, 49t Membrane(s), 552, 573 biosynthesis of lipids of, 780–81 fatty acids in, 479t role of lipids in structure, 547, 552–53 transport across, 552, 554b Memory, 621b Memory cells, 814 Mendeleev, Dmitri (1834–1907), 4, 43–44 Menstrual cycle, hormones and, 565 Mental disorders, 71, 585 Menthol oxidation product, 406 peppermint flavor, 362, 406 Menthone, 406 Mercaptan, 411, 415 2-Mercaptoethanol (HOCH2CH2SH), 607 Mercury(II) oxide, decomposition of, as endothermic reaction, 133 Messenger RNA (mRNA), 676, 691 properties of, during transcription and translation, 680 protein synthesis and role of, 703 transcription of, 697, 698 translation and role of, 700 Metabolic acidosis, 268b Metabolism, 726, 726–46, 743 anabolic pathway of, 728 See also Anabolism catabolic pathways of, 727, 728 See also Catabolism chemical energy (ATP) conversion into other energy forms in, 742–46 chemiosmotic pump and ATP production in, 739–40 citric acid cycle’s role in, 733–37 electron transport in, 737–39 H1 transport in, 737–39 mitochondria’s role in, 728–29 principal compounds of common catabolic pathway, 730–33 signal transduction effects on, 757b Metal(s), 44, 44–45, 46, 61 alkali, 47 See also Alkali metals binary ionic compounds named from, 77–78 cations named from, 72t reaction of acids, 251 use of, as historic landmarks, 47b Metal-binding fingers of transcription factors, 712 Metal hydroxides, 251 Metal ion coordination, 598–99, 609 Metalloids, 46, 46, 61 Metal oxides, acid reactions with, 251 Meta (m) locator, 385, 393 Meteorites, 47b, 285b Meter (m), Methadone, 450b Methamphetamines, 442b Methanal, 458 Methandienone, 566b Methane chlorine and, reaction between, 343 oxygen and, reaction between, 342–43 structure of, 94, 324 Methanethiol (CH3SH), 411 Methanol (CH3OH), 195, 413 COH bonds polarity in, 401–2 model of, 398 reaction of formaldehyde and hydrogen to produce, 221 structural formula, 311t Methenolone, 566b ■ I14 Methionine, 582, 701, 714 Methionine enkephalin, 626 Methoxycyclohexane, 408 Methyl, 330 Methylacetylene, 356 Methylamine, 316, 441, 447 hydrochloric acid and, reaction between, 253 structural formula, 311t Methylammonium hydroxide, 447 3-Methylaniline, 444 2-Methyl-1,3-butadiene (isoprene), 359 3-Methylbutanal, 458 3-Methylbutanoic acid (Isovaleric acid), 476 3-Methyl-1-butyne, 355 Methylcyclohexane, 337, 458 Methyleneimine, 311t Methyl ethyl ketone (MEK), 461 1-Methylguanosine, 677 5-Methyl-3-hexanone, 458 4-Methyl-1-hexene, 355 4-Methyloctane, 329 Methyl orange as pH indicator, 258 3-Methylphenol, 389 2-Methylpropane, 326 2-Methyl-1-propanethiol, 411 2-Methyl-1-propanol, 398 2-Methyl-2-propanol, 398, 403 2-Methylpropene, 403 Metric system, 8, 26 basic units in, 9t conversion factors between English system and, 10t heat measurement in, 22 length measurement in, 8–9 mass measurement in, 10–11 prefixes in, 9t temperature measurement in, 11–12 time measurement in, 11 volume measurement in, 9–10 Mevalonate, 781 Micelles, 483, 483 Micro RNA (miRNA), 678, 691 Mifepristone (RU 486), 565, 568 Millimeters of mercury (mmHg), 143 Millirem, 290 Milstein, César, 822 Mineralocorticoids, 564 Mineral oil, 340 Minerals, 795, 798t–802t See also specific mineral Mini-satellites, DNA, 679 Minor groove, B-DNA, 674 Mirror images of molecules, 421, 421, 423, 437 Miscible solutions, 181 Mitchell, Peter (1920–1992), 739 Mitochondria, role in cell catabolism, 728, 729, 743 Mixture(s), 34, 35, 61, 196t See also Colloids; Solution(s); Suspensions Molarity (M), 185–88, 204 Molar mass, 110–11, 133 Molecular collisions chemical reactions resulting from, 213–14 energy of, 213 kinetic molecular theory on, 152–53, 171, 219 Molecular weights (MW), 109, 109–10, 133 Molecule(s), 34, 35 See also Attractive forces between molecules; Compound(s) biological See Biomolecule(s) conformations of, 334, 335 functional groups in See Functional groups gases, and kinetic molecular theory, 152–53 handedness of See Chirality liquids, behavior of, 157–63 mirror images of, 421, 421 polarity of, 97–99, 100 I15 ■ Index predicting bond angles in covalent, 92–96 superposable, and nonsuperposable, 422 with two or more stereocenters, 430–34 Mole (mol), 110, 133 calculating mass relationships using, 110–14 defined, 110 one-mole quantities of select metals and compounds, 111 Molina, Mario, 345b Mollusks, shell construction in, 127 Monatomic anions, 72, 99 Monatomic cations, naming, 71–72 Monatomic elements, 36 Monoamine chemical messengers, 649–50 See also Dopamine; Epinephrine; Histamine; Norepinephrine (noradrenaline); Serotonin action of, 650 inactivation of, 652 Monoamine oxidases (MAOs), 652 Monoclonal antibodies, 822 cancer therapy using, 821b production of, 822 Monoglycerides, 548 Monomers, 370, 375 Monoprotic acids, 244 Monosaccharides, 517–33, 518, 539 amino sugars, 521–22 blood types and, 532b–533b carbohydrate breakdown to form, 748 characteristic reactions of, 527–33, 540–41 cyclic structures of, 522–27 D and L forms of, 519–21 defined, 518 D-Monosaccharide, 519, 520t, 539 extraction of energy from See Glycolysis Fischer projection formulas for, 518–19 galactosemia as inability to utilize, 522b L-ascorbic acid to, 526b nomenclature for, 518 physical properties of, 522 processing of, 792 structure for, 518 Montreal Protocol, 345b MOPS buffer, 267, 269t Morphine, 626, 655 Morton, W T G., 410b Movement, role of proteins in muscle, 579 Mullins, Kary B (1945–), 689 Multiple sclerosis, 556, 558b, 829 Multipotent stem cells, 834b Murad, Ferid, 654b Muscle(s), 435 contraction of, 742 enantiomer of lactic acid in, 435 enzymes and relaxation of, 616b lactate accumulation in, 752b proteins and, 579 storage of oxygen in, by myoglobin, 606b Muscone, 461b Mutagens, 716, 723 Mutarotation, 527, 540 Mutations, 715, 715–17, 723 biochemical evolution and gene, 715b silent, 716b in V(J)D gene, 820 Myelin sheath, multiple sclerosis and other diseases affecting, 558b Mylar polyester, 511 Myocardial infarction, 563, 629 Myoglobin, 606b Myrcene (bay oil), 362 N NADH glucose catabolism and, 753–54 NAD1 reduction to, 731, 735, 736, 755 NAD1 (nicotinamide adenine dinucleotide), 491, 743 in biological oxidation-reduction reactions, 731 reduction to NADH, 731, 735, 736, 755 structure of, 732 NADPH, pentose phosphate pathway, 752–53 NADP1 (nicotinamide adenine dinucleotide phosphate), 753 Naming See Nomenclature Nandrolone decanoate, 566b Nanotubes, 164, 195 Naphthalene, 386 Naproxen, 437 Natural gas, 332, 346 Natural killer (NK) cells, 809, 810, 814, 836 Negative modulation, 626 Neon (Ne), orbital box diagram for, 54 NER (nucleotide excision repair), 689, 717 Nerve cell anatomy, 640, 642 myelination of axons of, 558b Nerve gases, 641t Nerve transmission, drugs affecting, 641t Net ionic equation, 125, 134 Network solids, 165 Neurofibrillar tangles, 600b, 647b Neuron, 640, 642 See also Nerve cell Neuropeptide Y, 655 Neurotransmitters, 640, 661 amino acids as, 649 cholinergic, 641, 641–48 classification of, 641–43 effects of cocaine on, 632b excitatory, and inhibitory, 649 regulation of, 648, 652 removal of, 652 signal transduction and, 650, 651 Neutralization as property of acids and bases, 251 Neutralizing antibody, 835 Neutral solution, 256, 270 Neutron, 38, 39, 61 in isotopes, 280 Nicotine, 443b, 644, 648 Nicotinic receptor, 644 Niemann-Pick disease, 560t Nirenberg, Marshall (1927–), 700 Nitration of benzene and derivatives, 387–88, 394 Nitric acid (HNO3), 243b Nitric oxide (NO) as air pollutant, 88b macrophage function and, 814 as secondary chemical messenger, 88b, 654b 4-Nitroaniline, 444 Nitrobenzene, 388 4-Nitrobenzoic acid, 388 Nitrogen catabolism of amino acid, 760–64 Haber process and conversation of, to ammonia, 234b Nitroglycerine (trinitroglycerin), 389b, 401b Nitrous oxide, 410b N-Methylacetamide, 499 N-Methyl-D-aspartate (NMDA) receptor, 649 Nobel, Alfred (1833–1896), 401b Noble gases, 48 melting and boiling points of, 49t notations, 54–55, 57t octet rule for electron configuration, 69t Nomenclature See also IUPAC naming system alcohols, 398–400 aldehydes and ketones, 458–61 alkanes, 328–31 alkenes and alkynes, 355–61 amines, 444–46 aromatic compounds, 384–87 binary ionic compounds, 77–78 carboxylic acids, 475–78 common, 331, 331–32 See also Common names enzymes, 616 ethers, 408–9 glycosides, 528 ionic compounds containing polyatomic ions, 79 monatomic cations, 71–72 monoatomic anions, 72 polyatomic ions, 72 thiols, 411–12 Nonbonding electrons in Lewis dot structures, 83 Noncompetitive inhibitors of enzymes, 618, 620, 621, 623, 633 Nonelectrolytes, 192 Nonmetals, 46, 46, 61 Nonpolar covalent bonds, 80, 80–81, 100 Nonspecific immune-system cellular interactions, 813t Nonsteroidal anti-inflammatory drugs (NSAIDs), 502b, 570, 571b, 572 See also Aspirin Nonsuperposable molecules, 422 Norepinephrine (noradrenaline), 449 absorption of, into receptor site, 650, 651 drugs affecting messenger function of, 641t oxidation of, to aldehyde, 652 reaction between hydrochloric acid and, 449 Norethindrone, 568b Norethynodrel, 568b Normal boiling point, 161 Novocain, 450b N-terminus (N-terminal amino acid), 589, 593 Nuclear chemistry, 276–306 detection and measurement of nuclear radiation, 286–89 emission of radioactivity by atom nucleus, 279–83 nuclear fission and atomic energy, 298, 298–99 nuclear fusion, 296, 296–97 nuclear half-life, 284–86 nuclear medicine, 292–96 radioactive dating, 285b radioactivity, 276–79 relationship of radiation dosimetry to human health, 289–91 Nuclear energy, 20 accidents involving, 286, 300b fission, 298, 298–99 fusion, 296, 296–97 Nuclear equation, balancing, 280–81 Nuclear fission, 298, 298–99, 301, 301 Nuclear fusion, 296, 296–97, 301 Nuclear medicine, 292–96 medical imaging, 292–95 radiation therapy, 295–96 Nuclear power plant accidents, 286, 300b Nuclear reaction, 280 Nuclear weapons testing, health hazard of, 45b Nucleic acids See also Deoxyribonucleic acid (DNA); Ribonucleic acid (RNA) structure of, 666–69, 670–72 See also Nucleotide(s) of viruses, 709b Nucleophilic attack DNA replication and, 683 enzyme mechanisms and, 623 peptide bond formation and, 706 Nucleosides, 667, 669, 669t Nucleosomes, 674, 691 Nucleotide(s), 668, 669, 671 bases of, 666, 666–67 DNA replication, and addition of, 683 eight, in DNA and RNA, 669t excision repair of, 687–89 Okazaki fragments of, 686 phosphate of, 668–69 sequences of, in DNA, 675 See also Nucleotide sequences in DNA sugars of, 667–68 Index Nucleotide excision repair (NER), 689, 717 Nucleotide sequences in DNA, 675 coding and noncoding (exons, introns), 679, 680, 698, 698 satellite, 679 Nucleus (atom), 38, 39 half-life of radioactive decay, 284–86 radioactivity emission by, 279–83 Nucleus (cell), 729 Numbers, notation of, 5–7 Nutrients, 787 classification of, 788 disease caused by insufficient, 782b, 791, 795 essential amino acids, 782, 782b, 795 essential fatty acids, 548, 794 food guides on, 789, 790b food labels listing, 788 minerals as, 795, 798t proteins, 795 recommended daily allowances of, 788, 791 requirements for, 799t–802t structure of, 799t–802t vitamins, 795, 798t water as, 805 Nutrition, human, 787–808 See also Diet, human athletic performance enhancement and, 803b calorie count and, 791–92 carbohydrate processing, 792–94 dietary protein processing and, 794–97 fats processing, 481b–482b, 794 measurement of, 787–91 minerals, 797–805 protein complementation, 795 vitamins, 797–805 water, 797–805 Nylon-66, 510 O Obesity biological basis of, 779b dietary fats and, 481b health dangers of, 791–92 weight-reduction drugs, 738b Octanal, 406 Octane rating, 343b Octanoic acid, 406 1-Octanol, 406 Octet rule, 69, 70, 99 exceptions to, 86–87 Octyl p-methoxycinnamate, 506b Odors See Scents and odors —OH (hydroxyl) group, 314, 389, 398, 414 -oic acid (suffix), 476, 499 Oils, 548, 572 percentage of fatty acids in select common, 549t rancidity of, 550b Oil spills, 18 Okazaki fragments, 686, 691 Oleic acid, 549 Olestra, 796b–797b Oligosaccharides, 533 -ol (suffix), 398, 414 Omega-3 fatty acids, 481b Oncogenes, 717b Open complex, 710 Optically active compounds, 434, 434–35, 437 Oral contraception, 568b Orbital(s), 50, 61 distribution of, within shells, 50t energy levels for, 51 rules governing, 51–52 1s, 2s and 2p, 51 shapes and spatial orientation of, 51 Orbital box diagrams, 52–54, 53t Organelles, 729, 743 Organic chemistry, 308–22 functional groups, 313–18 introduction to, 308–9 obtaining organic compounds for, 309–11 writing structural formulas, 311–13 Organic compound(s) isolation of, from nature, 309 properties of inorganic and, compared, 309t structural formulas for, 311–13 synthesis of, in laboratory, 309–11 Origin of replication, 680 Orinase (Tolbutamide), 659b Ornithine, 615, 762, 763 Ortho (o) locator, 385, 393 -ose (suffix), 518, 528 Osmolarity, 200, 204 Osmosis, 199–200, 201b Osmotic membrane, 199 Osmotic pressure, 199, 199–203, 204 Ovulation, 565 Oxalic acid, 476 Oxaloacetate, 736 from malate, 736 from PEP, 758 Oxalosuccinate, 734–35 Oxalosuccinic acid, 491 Oxidation, 128–33, 134 See also Redox reactions b-, 748, 755–57, 768 of aldehydes and ketones, 462–63, 469 of alkanes, 342, 346 bile salts as product of cholesterol, 569 defined, 128 of fats and oils, and resulting rancidity, 550b of monosaccharides, 529–31, 541 obtaining energy from fatty acids by b-oxidation, 748, 755–57, 768 of primary and secondary alcohols, 405–6, 415 of thiols, 413, 415 Oxidation–reduction reaction, 128, 731 See also Redox reactions Oxidative damage, protection against, 753 Oxidative deamination, 761, 761–62, 764, 768 Oxidative phosphorylation pathway, 730, 741, 743, 749, 754 uncouplers of, 738b Oxidizing agents, 128, 133 antiseptics as, 132b Oxidoreductases, 616, 617t 3-Oxobutanoic acid, 492b Oxonium ion, 367 Oxygen (O2) alkanes and, reaction between, 342–43 hemoglobin and myoglobin behavior when binding, 605b–606b hyperbaric chambers for deprivation of, 151b orbital box diagram for, 54 steel wool and, chemical reaction between, 217 Oxytocin, 655 function, 594–95 structure, 595 Ozone (O3) chlorofluorocarbons effects on, 345b as oxidizing agent, 132b P p53, 717b Paclitaxel (Taxol), 310b Padimate A, 506b Pain signals, transmission of, 655–56 Papain, 623, 625 Paraffin wax, 340, 340 Para (p) locator, 385, 393 Parkinson’s disease, 586, 653b Partial pressures, Dalton’s law of, 150–52 Parts per billion (ppb), 190 ■ I16 Parts per million (ppm), 190–91 Pascal, 143 Passive transport, 554b Pasteur, Louis, 825b Pauling, Linus, 74, 596 structure of benzene by, 383 theory of resonance by, 89, 383 Pauling scale, 74t Penicillins, 501b enzyme inhibition by, 623 1,4-Pentadiene, 359 Pentanal, 464 Pentane (C5H12), 163, 325, 331 1,5-Pentanediamine (cadaverine), 446 Pentanedioic acid (glutaric acid), 476 Pentanoic acid, 479 1-Pentanol, 464 Pentobarbital, 508b Pentose phosphate pathway, 752, 752–53, 753, 768 Pent- (prefix), 518 Peppers, capsaicin in, 392b PEP (phosphoenolpyruvate), 758 Pepsin, 618, 794 Peptide(s), 590 as chemical messengers, 643, 655–57 human disease caused by conformation changes in, 600b protein synthesis from See Protein synthesis side chains of, 590 Peptide bond, 587–90, 608 formation of, in protein synthesis, 704, 706 Peptide linkage, 587 Peptidergic chemical messengers, 643, 655–57, 661 Peptidyl transferase, 704, 705 Percent concentration (%w/v) of solutions, 184–85, 204 Percent yield of product mass in chemical reactions, 123, 134 Periodic properties, 57–60 atomic size, 57–58 ionization energy, 58–60 Periodic Table, 4, 43–49, 61 classification of elements in, 46 inner transition elements in, 44 main-group elements in, 44 origin of, 43–44 periodicity in, 47–49, 57–60 relationship of electron configuration, to position in, 56–57 transition elements in, 44 Peroxidase, 631b Peroxide, 372 Personal genomics, 685b Pesticides, 500b PETN (pentaerythritol tetranitrate), 389b Petroleum, 332, 346 fractional distillation of, 332, 332 ocean spills of, 18 pH (hydronium ion concentrations), 256–58, 270 of buffers, 263–64, 265–67 enzyme activity and, 619 of human blood, 257, 265 indicators of, 258, 258t, 259 isoelectric point (pI), 584, 591–92, 592 values of, for select common materials, 258t Phagocytes, 816 Phagocytosis, 816 Pharmaceutical drugs See also Drugs analgesics, 502b antibiotics, 295, 424b, 501b, 828b antihistamines, 655 antiviral, 709b, 832 body mass effects on dosage of, 11b bronchodilators, 451b I17 ■ Index chemical communications and nerve transmissions affected by, 640–41, 641t chemotherapy, 817b diabetes mellitus, 659b enantiomer, 421, 424b genetic variation in responses to, 687b ionic compounds in, 80b lithium, for depression, 71 MAO inhibitors, 652 monoclonal antibodies, 821b nitroglycerin, 401b statin drugs, 781 time-released, 222b tranquilizers, 446b weight-reducing, 738b Pharmacogenomics, 687b Phase, 166, 171 Phase change, 166, 171 Phase diagram, 168, 170 for water, 168 Phenanthrene, 386 Phencyclidine (PCP), 649 Phenobarbital, 508b Phenol(s), 384, 389–93, 402 acidity of, and reaction with bases, 390, 394 as antioxidants, 390–93 structure and nomenclature, 389–90 Phentermine, 442b 2-Phenylacetamide, 508 Phenylalanine, 582, 586, 765, 795 faulty catabolism of, in humans, 766b genetic code and, 700 Phenyl group C6H5, 384 Phenylketonuria (PKU), 766b pH indicator, 258, 258t, 259 Phosgene, 511 Phosphate as buffer, 265 nucleic acids, 668–69 solubility of, 127t transfer of phosphate groups, in common catabolic pathway, 730–31 Phosphatidylcholine, 553, 554b, 780 Phosphatidylethanolamine, 553 Phosphatidylinositol 4,5-bisphosphates (PIP2), 555 Phosphatidylinositol (PI), 555, 555 Phosphatidylserine, 553 Phosphine, 86 Phosphoenol pyruvate (PEP), 622b Phospholipids, 551, 572 See also Glycerophospholipids; Sphingolipids Phosphoric acid (H3PO4), 86, 243b Phosphoric anhydrides, 510 Phosphoric esters, 510, 531 Phosphorus (P), 54 Phosphorus pentachloride, 86 Phosphorylated protein kinase, 712 Phosphorylation, 730 of enzymes, 627 in glycolysis process, 748–52 Photofrin (drug), 607b Photons, 278 Photorefractive keratectomy (PRK), 607b Photosynthesis, 773, 775b–776b, 784 Physical changes, 2, 26 Physical properties, of alcohols, 400–402 of aldehydes and ketones, 461–62 of alkanes, 340–42 of alkenes and alkynes, 361–62 of amines, 446–47 of carboxylic acids, 478–79 of colloids, 196t, 197–203 of ethers, 409–10 of monosaccharides, 522 of solutions, 179–81, 196t of suspensions, 196, 196t of thiols, 412 of triglycerides, 548–49 Picropodophyllin, 817b Piperidine, 442 PIPES buffer, 269t Pituitary hormones, 643 pKa (acid strength) See Acidity Plane-polarized light, 434–35, 437 Plant(s) anabolism in, 775b–776b cellulose in, 536–38, 578 ethylene as regulator of growth in, 353b photosynthesis and carbohydrate biosynthesis in, 773 terpenes in essential oils of, 362 Plasma, 201 Plasma cells, 814, 819 Plasmids, 718, 719 Plastics polyethelene, 370–73 recycling of, 374b a-Pleated sheet, 597 b-Pleated sheet, 596, 597, 609 Pluripotent stem cells, 834b PM (poor metabolism) of drugs, 687b pOH (OH2 concentrations), 256–58, 270 Point mutations, 820, 822 Poison(s) disrupted chemical messaging by, 648 puffer fish, 337b Poison ivy, 390 Polar compounds in solutions, 182 solvation of, by water, 195 Polar covalent bonds, 80, 80–81, 100 Polarimeter, 435, 437 Polar molecules, 97–99, 100 Pol II transcription factor, 710, 711 Poliomyelitis virus, 709b Polyamides, 510 Polyatomic elements, 37, 37 Polyatomic ions, 72, 99 ionic compounds containing, 79 names of common, 72t Polycarbonates, 511 Polyenes, 359–60 Polyesters, 510–11 Polyethylene, 370–73, 371t low-density, and high-density, 372–73 recycling, 374b Poly(ethylene terephthalate) (PET), 510–11 Polymer(s), 370, 375 chain-growth, 370 important, derived from ethylenes, 371t Polymerase chain reaction (PCR), 689, 690, 691 Polymerases, 697 Polymerization, step-growth, 509, 509–11 Polymerization reactions of ethylenes, 370–73, 376 Polynuclear aromatic hydrocarbons (PAHs), 386–87, 387b, 393 Polypeptides, 590, 609 Poly- (prefix), 371 Polysaccharides, 533, 536–38 acidic, 538–39 cellulose as, 536–38 glycogen as, 536 starch (amylase, amylopectin) as, 536 Polyunsaturated oils, 549 Polyvinyl chloride (PVC), 371 Positive cooperativity, oxygen binding by hemoglobin and, 605b Positive modulation, 626 Positron emission, 282–83, 300 Positron emission tomography (PET), 294, 295 Postsynaptic membranes, 640, 642, 661 Post-transcription stage, 699, 713 Post-translational modification, 586 Post-translation stage of gene regulation, 713 Potassium bicarbonate, 252 Potassium hydroxide (KOH), 251 Potassium permanganate solution, 188 Potassium sulfate (K2SO4), 125 Potential energy, 20, 26 kinetic energy, conversion of to, 20 Pre-initiation complex, 703, 710 Prenylation, 780 of ras protein, 781b Pressure, 143 effect of change in, on chemical equilibrium in gases, 233–35 partial, Dalton’s law and, 150–52 solubility of gases and, 182 standard temperature and, 148–49 temperature and, in gases, 146 vapor, of liquids, 158–61, 161 volume and, in gases, 144, 144 Presynaptic nerve ends, 642, 661 Priestley, Joseph, 410b Primary (1°) alcohol, 314, 399, 414 oxidation of, 405–6, 415 Primary (1°) amine, 315, 441, 452, 476 Primary structure of protein, 593, 593–95, 603, 609 Primases, 686 Primer(s), nucleic acid hybridization of DNA, 691 RNA, 683, 686 Principal energy levels, 51, 61 Prion proteins, 600b Products in chemical reactions, 109 Proenzymes (zymogens), enzyme regulation by, 626, 634 Progenitor cells, 834b Progesterone, 564, 661 biosynthesis of hormones from, 564 female reproductive cycle and, 565 Prokaryotes gene expression in, 696 properties of mRNA molecules in, during transcription and translation, 680 ribosome structure in, 678 Proline, 581, 587 Proline racemase, 629–30, 631 Promoters, 698, 710, 723 Pro Osteon, 73b 2-Propanamine, 444 Propane (CH3CH2CH3) balancing equation for, 115 combustion of, 114, 114 condensed structural formula, model, and line-angle form, 325 reaction of oxygen with, 343 Propanedioic acid (malonic acid), 476 1,2-Propanediol (propylene glycol), 400 1,2,3-Propanetriol (glycerin), 400, 401b, 482 2-Propanol (isopropyl alcohol), 315, 398 Propanone (acetone), 458 See also Acetone (C3H6O) 2-Propenal (acrolein), 458 Propene acid-catalyzed hydration of, 367 polymerization of, 371 structure of, 354 Propofol, 531 Proportional counter, 287 Propylamine, 445 Propylene, 356 Propylene glycol, 400 Index Prostaglandin(s), 569, 569–72, 573 Prostaglandin enderoperoxide synthase (PGHS), 631b Prosthetic group, 601 Proteasomes, post-translational gene regulation and, 713 Protein(s), 578–611 allosteric, 605b amino acids, 579–83 See also Amino acid(s) binding, 697 chaperone, 601, 608 combined amino acids to form, 587–90 complement of, expressed by genomes, 602b complete, 795 conjugated, 601 denatured, 605–8 enzymes as, 4, 579 See also Enzyme(s) fibrous, 579 functions of, 578–79 gap junctions constructed of subunits of, 554b globular, 579 human body processing of, 794–97 human disease caused by conformation changes in, 600b integral membrane, 604 isoelectric point, 584, 591–92, 592 metabolism of See Protein catabolism modification of, and enzyme regulation, 627 prenylation of, 781 primary structure of, 593, 593–95, 603 properties of, 590–93 protective function of, 579 quaternary structure of, 601–4, 605b–606b secondary structure of, 596, 596–97, 603 synthesis of See Protein synthesis tertiary structure of, 598–600, 603 zwitterions, 583, 583–84, 592 Protein anabolism, 782–84 See also Protein synthesis Protein catabolism, 748, 760–65 amino acid carbon skeleton processing in, 764–65 heme catabolism, 766–67 nitrogen processing in, 760–64 overview, 760 Protein–cofactor complexes, 773 Protein complementation, 795 Protein kinase M, 621b Protein microarrays, 602b Protein modification, enzyme regulation and, 627, 634 Protein synthesis, 702–8 See also Gene expression activation stage, 702–3 biosynthesis of amino acids and, 782–84 elongation stage, 703–6 genes and, in prokaryotes versus in eukaryotes, 679, 680 hereditary information in DNA for direction of, 666, 670, 696 initiation stage, 703, 704 molecular components of reactions at four stages of, 702t role of different RNAs in, 677–78, 678t termination stage, 706, 707 Proteome, 602b Proton(s), 38, 39, 61 in isotopes, 280 properties of, and location in atoms, 38t Proton channel, 737, 740 Proton gradient, 739 Proton-translocating ATPase, 740, 743 Proust, Joseph (1754–1826), 36 Prusiner, Stanley, 600b P site, ribosome, 703 Psoriasis, 829 Puffer fish, tetrodotoxin and poisonous, 337b Purines, 442, 721 in DNA and RNA nucleotides, 666–67, 672–73, 673 Pyramidal molecular shape, 93 -pyran-, 523 Pyranose, 523, 539 Pyrethrins as natural insecticide, 500b Pyridine, 442 Pyridoxal phosphate, 510 Pyrimidine, 442 in DNA and RNA nucleotides, 667, 673, 673 Pyrrolidine, 442 Pyruvate, 465, 622b, 628, 783 amino acid carbon skeleton catabolism and production of, 764–65 glycolysis and production of, 749, 750 oxidative decarboxylation of, and production of acetyl CoA, 752 Pyruvate dehydrogenase, 752 Pyruvate kinase active site and substrates of, 622b model of, 622b phosphorylation, 627 regulation of glycolysis by, 749 Q Quaternary structure of proteins, 601, 601–4, 609 allosteric proteins and, 605b–606b hemoglobin, 601, 604 R R, S system, 427, 427–30, 437 applied to ibuprofen, 430 meaning of R and S in, 427 priorities for some common groups, 427t Racemic mixture, 424, 424b, 437 Radiation dosimetry, human health and, 289–91, 290t, 291, 291t Radiation therapy, 295–96 Radical (free radical), 390 formation of, from nonradical, 391 reaction of, to form new radical, 392–93 tissue damage caused by, 293b Radioactive dating of archeological objects based on, 285b Radioactive isotopes, 279, 280 Radioactive materials, 279 Radioactivity average exposure to, from common sources, 291t detecting and measuring nuclear, 286–89 discovery of, 276–77 electricity and, 277–78 half-life of, 284–86 human health and, 289–91, 293b particles and rays encountered in, 279t three types of, 277–79 Radon, health hazard from indoor pollution caused by, 292b Rads, 289–90, 290t, 301 Rain, acid, 180b R— (alkyl group), 329, 329t, 346 Rancidity of fats and oils, 550b Random coils, protein, 596, 597, 609 Rate constant, 218 Rate of reaction, 222, 235 See also Chemical reaction rates RDX (cyclonite), 389b Reactants See Chemical reactant(s) Reaction mechanism, 365, 375 Receptors of chemical messages, 640, 661 amino acid, 649 cholinergic (acetylcholine), 644 Recombinant DNA techniques, 718–20, 723 Recommended Daily Allowances (RDA) of nutrients, 788, 789, 799t–802t ■ I18 Recycling plastics, 374b Red blood cells (erythrocytes) destruction of aged, 766 sickle cell anemia and, 595, 596b, 679, 716 Redox reactions, 128–33 important categories of, 130–33 Reducing agent, 128 Reducing sugars, 529, 540 Reduction, 128–33, 134 See also Redox reactions of aldehydes and ketones, 463–65, 470 of alkenes, 370, 376 of carboxylic acids, 488, 493 defined, 128 of monosaccharides to alditols, 529, 541 Regioselective reactions, 364 Regulator of allosteric enzyme, 626 Regulatory portion of eukaryotic gene, 698 Regulatory site, enzyme, 626 Rems, 290, 301 Replication, DNA, 676, 679–86, 696 general features of, 683, 686 leading and lagging strands in bidirectional, 681, 686 origin of, 680 replication fork, 680, 686 replisomes in, 683 semiconservative nature of, 681 steps of, 683, 686 Replication, RNA, 696 Replication fork, 680, 686 Replisomes, 683 components of, and functions, 683b Residues, amino acid, 590 Resonance, 89–92, 100 theory of, 89–91 writing acceptable contributing structures, 91–92 Resonance hybrids, 89, 90, 383 Resonance structure (resonance contributors), 89, 383–84 See also Contributing structures Respiration as oxidation reaction, 130, 130–31 Respiratory acidosis, 268b Response elements, 710 Restriction endonucleases, 719 Retinol, human vision and, 361b Retrovaccination, 836 Retroviruses, 830 Reuptake, 649, 661 Reverse denaturation, 608 Reverse desalinization, 201b Reverse osmosis, 201b Reverse transcriptase, 831, 831 Reversible chemical reactions, 221, 221–22 Rheumatic fever, 828b Rheumatoid arthritis, 538, 829 Rhodopsin, 780 Ribofuranose, 524 b-D-ribofuranose (b-D-Ribose), 528, 667 Ribonucleic acid (RNA), 666, 691 bases of, 666–67 classes of, 676–78 nucleotides and nucleosides of, 669t phosphate of, 668–69 primer, in DNA replication, 683, 686 roles of different kinds of, 678t splicing of, 678, 680, 713, 713 structure of DNA and, 670–76 sugars of, 667–68 transcription of DNA information to See Transcription translation and role of, 699–700 Ribose, 527, 667 pentose phosphate pathway and production of, 752–53 I19 ■ Index Ribosomal RNA (rRNA), 677–78, 678t, 691, 696 See also Ribosomes post-transcription methylation of, 699 translation and role of, 699–700 Ribosomes, 677, 677–78 protein synthesis in, 699–700, 703–6 role as ribozyme, 706 40S ribosome, 700 60S ribosome, 700 structure of prokaryotic, 678 Ribozymes, 614, 678, 691, 706 Rivastigmine, 648b RNA See Ribonucleic acid (RNA) RNA polymerases, 697, 699 Rodbell, Martin (1925–1998), 650 Roentgens (R), 289, 290t Röntgen, William, 277 Rowland, Sherwood, 345b R (relaxed) form of enzyme, 626, 627 RU 486 (Mifepristone), 565, 568 Rusting as redox reaction, 131, 131–32 S Saccharides, 518 disaccharides, 533–35 monosaccharides See Monosaccharides oligosaccharides, 533 polysaccharides, 536–38 Saccharin, 796b Salicin, 502b Salicylic acid, 502b, 507 Salmeterol, 451b Salt bridges, tertiary protein structure stabilized by, 598, 599, 609 Salts as product of reactions between acids and ammonia/amines, 253, 270 soaps and formation of, 483 Saponification, 482, 504 of fats, 550–51 Sarcoplasmic reticulum, 554b SARS (severe acute respiratory syndrome), 830 Satellites, DNA, 679 Saturated fats, 479t, 480, 548, 549t, 563 Saturated hydrocarbons, 324, 346 Saturated solution, 181 Scents and odors, 412, 446 aromatic compounds See Aromatic compounds carboxylic acids, 479 Schultz, Peter, 630 Schwann cells, 558b Scientific method, 3–5, 26 Scintillation counters, 287 Screening for alcohol on human breath, 407b Seaborg, Glenn (1912–1999), 297, 297 Second (s), measurement of, 11 Secondary (2°) alcohol, 314, 399, 414 oxidation of, 406 Secondary (2°) amine, 315, 441, 452 Secondary messengers, 640, 643, 650–51, 661 See also Prostaglandin(s); Thromboxanes action of peptidergic messengers, hormones, and neurotransmitters and role of, 656–57 calcium as, 645b cyclic AMP (cAMP) as, 650–51 nitric oxide as, 654b steroid hormones as, 642–43 Secondary structure of proteins, 596, 597–98, 603, 609 extended helix of collagen, 598 a-helix, and b-pleated sheet, 596, 597, 597, 609 Second genetic code, 703 Seeding, 182 Selenocysteine, 708b Semiconservative replication of DNA, 681 Semipermeable membrane, 199 Sense strand, 697 Serendipity, defined, Serine, 555, 581 Serotonin, 585, 650, 653b drugs affecting messenger function of, 641t Severe combined immune deficiency (SCID), 721, 811 Sex hormones, 565–68, 573 Sex pheromones, 358b Shells (atom), 51, 61 distribution of electrons in, 50t distribution of orbitals within, 50t valence, 55 Shine-Dalgarno (RNA) sequence, 703, 704 Shroud of Turin, dating of, 285b SH (sulfhydryl) group, 411 SI See International System of Units (SI) Sickle cell anemia, 595, 596b, 679, 716 Side chains, peptide, 590 Side reactions, 123 Sievert, 290 Sieving portions of enzyme, 714 Sigmoidal curve, 606b Signal transduction, 650, 651, 661 in DNA replication, 683 effects of, on metabolism, 757b removal of signal amplification and, 651–52 Significant figures (numbers), 6, 6–7, 26 Silencers (DNA sequences), 710 Silent mutations, 716b Silicon in microprocessor chips, 120 Silk, 597b Silver acetate, 230 Silver chloride (AgCl), 125 reaction with sunlight, 233b Silver cyanate, urea produced from reaction between ammonium chloride and, 308 Silver-mirror test, 463 Single bond, 79, 83 Skunk, scent of, 412 Small interfering RNA (siRNA), 678, 691 Small nuclear ribonucleoprotein particles (snRNPs), 678, 691 Small nuclear RNA (snRNA), 678 Smallpox, 825b Smelting of ores, 180b Smoking, carcinogenic polynuclear aromatics and, 387b Snake venom, 648 Soaps, 479–84, 551, 572 See also Detergents cleaning function of, 483–84 fatty acids and, 479–82 micelles and, 483 saponification of fats and production of, 551 structure and preparation of, 482–83 Sobrero, Ascanio (1812–1888), 401b Sodium acetate, 505 Sodium benzoate, 486 Sodium bicarbonate, 245 Sodium borohydride (NaBH4), 464 Sodium carbonate, reactions between acids and, 251 Sodium chloride (NaCl), 68, 70, 71, 75 crystal structure, 76 solution of, 181 Sodium 4-dodecylbenzenesulfonate, 390, 484 Sodium ethanethiolate (CH3CH2S2Na1), 412 Sodium hydroxide (NaOH) (lye), 243b, 504 titration of sulfuric acid (H2SO4) with, 259 Sodium (Na), 46 atomic size, 57 orbital box diagram for, 54 Sodium pentobarbital (Nembutal), 508b Sodium phenoxide, 402 Sodium urate monohydrate in human joints as cause of gout, 193 Solenoid, 674, 675 Solid(s), 17, 26, 142, 142, 142 amorphous, 165 characteristics of various, 164–65 network, 165 phase change from, to gas, 166–70 solubility of, as function of temperature, 182 types of, 165t water of hydration in, 191 Solid hydrates, 191 Solidification, 153 Solid state, 142 See also Solid(s) Solubility, 181, 204 of alcohols, 402t of alkanes, 341, 402t of drugs in human body fluids, 450b as function of temperature, 182 of hydrochloric acid, 195 of sulfur trioxide, 195 Solute, 179, 204 nature of solvent and, 182 Solution(s), 178–95, 204 aqueous See Aqueous solution(s) characteristics and properties of, 179–81 concentration of See Concentration of solutions factors affecting solubility, 181–83 introduction to, 178–79 isotonic, hypertonic, and hypotonic, 202 most common types of, 179t properties of colloids, suspensions, and, 196t units for expressing concentration of, 184–91 water as superior solvent, 191–95 Solvated anions and cations, 191 Solvent(s), 179, 204 haloalkanes as, 345 nature of solute and, 182 water as, 191–95 Somatic cells, 681b gene therapy in, 721 telomeres in chromosomes of, 681b Somatic hypermutation (SHM), 820 Specific gravity, 19, 19–20, 26 Specific heat (SH), 22–25, 26, 166 for common substances, 22t of water, 23b, 166 Specific immune-system cellular interactions, 813t Specificity of enzymes, 615 Specific rotation, 435 Spectator ions, 125, 134 Sphingolipids, 551, 555, 555–56, 573 Sphingomyelin, 554b, 556, 780 Sphingosine, 555 Sphygmomanometer, 159b Spider silk, 578, 597b Splicing of RNA molecules, 678, 680 alternative, 713 Sports drinks, 569 Standard temperature and pressure (STP), 148 Starch, 536, 540 action of enzymes on, 792 States of matter, 2, 17–18, 141–42 See also Gas(es); Liquid(s); Solid(s) energies involved in phases changes in, 166–70 Stearic acid, 549, 757–58, 758t Steel wool, 217 Stem cells, 834b–835b development of lymphocytes from, 815 history of research on, 835b promises and potential of research on, 834b–835b Step-growth polymers, 509, 509–11 polyamides, 510 polycarbonates, 511 polyesters, 510–11 Index Stereocenters, 338, 424, 437 specifying configuration of, 427–30 stereoisomers, 430–34 Stereoisomers, 339, 421 of alkenes, 354, 359, 375 of amino acids in proteins, 580, 583 cis-trans, 337–39 See also Cis-trans isomers diastereomers, 421, 431 enantiomerism and, 339, 420–26 for molecules with two or more stereocenters, 430–34 Steroid(s), 558, 558–63, 573, 643 cholesterol, 561 See also Cholesterol lipoproteins and cholesterol transport, 561–63 physiological roles of, 564–68 structure, 560 Steroid hormones, 564–68, 657 adrenocorticoid, 564, 564–65 anabolic steroids, 566b–567b oral contraception, 568b as secondary messengers, 642–43, 657–58, 660–61 Sticky ends, DNA, 719 Stitches, dissolving surgical, 512b Stoichiometry, 118, 118–21, 134 limiting reagents and, 121, 121–22 percent yield calculations, 123–24 Stomach acid food catabolism and role of, 792, 795 human, use to antacids to relieve, 253b Storage proteins, 579 Strassman, Fritz (1902–1980), 298 Strep throat, 828b Strong acid, 242t, 245t Strong base, 242, 245t Strong electrolytes, 193 Strontium-90, 284 calcium, human bones, and, 45b Structural formulas, 83 of alkanes, 323–25 condensed, 314 for organic compounds, 311–13 Structural gene, 698, 698 Structural isomers See Constitutional isomers Structural proteins, 578 Styrene, 384 Subatomic particles, 38 Sublimation, 167, 171 Subshells, 50, 61 Substance P, 656 Substrate, 618–19, 633 concentration of, and enzyme activity, 618–19 Substrate specificity, 615 Succinate, 491, 736 Succinic acid, 476 Succinylcholine, 616b as competitive inhibitor, 648 Sucralose, 796b Sucrose (C12H22O11), 182, 195, 518, 533–34, 540 Sugars amino, 521–22 as component of nucleic acids, 667–68 glucose See Glucose reducing, 529, 540 table See Sucrose (C12H22O11) Sulfhydryl (SH) group, 411, 415 Sulfides, 127t Sulfonation of aromatic compounds, 388–89, 394 Sulfur mixture of iron and, 35 nucleophilic attack by, 623, 625 Sulfur dioxide (SO2), 87, 180b, 194b Sulfuric acid (H2SO4), 87, 180b, 243b Fischer esterification and, 501 titration of, with sodium hydroxide, 259 Sulfur trioxide (SO3), 180b, 194b Sumner, James, Sunglasses, 233b Sunscreens and sunblocks, 506b Supercritical carbon dioxide (CO2), 169b Superposable molecules, 422 Supersaturated solution, 181 temperature and, 182 Surface tension, liquids, 158, 171 Suspensions, 196 properties of colloids, solutions, and, 196t Sweeteners, artificial, 589b, 794, 796b–797b Sweetness, 535t Synapse, 640, 642, 661 Systolic blood pressure, 159b T Table salt See Sodium chloride (NaCl) Table sugar See Sucrose (C12H22O11) TATA box, 698, 710 Tatum, Edward (1909–1975), 666 Tau proteins, 647b Taurine, 569, 649 Taurocholate, 569 Tautomers, 468 Taxol, search for, and discovery of, 310b Tay-Sachs disease, 560t T cell(s), 811, 812, 836 See also T-cell receptor(s) cytotoxic (Tc cells), 814 growth and differentiation of, 827 helper, 814 See also Helper T cells (TH cells) interaction of, with dendritic cell, 814 memory, 814 self/nonself determination, and selection of, 826 T-cell receptor complex, 823, 824 T-cell receptor(s) (TcR), 811, 822–23 adhesion molecules of, 823 CD4 molecule and HIV infection, 824, 831 differences between immunoglobulins and, 823 peptide antigen recognition by, 815 structure of, 823, 823 Telomerase, 681b Telomeres, 681b Temperature body, 221b chemical equilibrium affected by, 232–33 chemical reaction rates affected by, 218–20 density and, 19 entropy and, 143b enzyme activity and, 619 fever, 219b heat and, 21–22 kinetic energy and, 142, 219 measurement of, 11–12 pressure and, in gases, 146 solubility of solids as function of, 182 standard pressure and, 148 vapor pressure and, 161 volume and, in gases, 146 Temperature scales, 11–12 Template strand, 697 Terbutaline, 451b Termination sequence, transcription process, 699 Termination stage of protein synthesis, 706, 707 Terpenes, 362–63, 375 Tertiary (3°) alcohol, 399, 414 oxidation of, 406 Tertiary (3°) amine, 315, 441, 452 Tertiary structure of proteins, 598, 598–600, 603 forces leading to formation of, 601 forces stabilizing, 598–600 TES buffer, 269t Testosterone, 565, 568 anabolic steroids and, 566b Tetracycline, effects of, 295 Tetrahydrofuran (THF), 409 ■ I20 Tetrodotoxin in puffer fish, 337b Tetr- (prefix), 518 Theoretical yield of product mass in chemical reactions, 123, 134 Theory, defined, 4, 26 Thermal cracking, 353 Thermal decarboxylation, 490–91 Thermal pollution, 182 Thermogenin, 738b Thiols, 411–13 functional group of SH (sulfhydryl) group, 411 nomenclature of, 411–12 physical properties of, 412 reactions of, 412–13, 415 structure of, 411 Threonine, 582 Threose, 431 Thromboxanes, 570, 573 Thudichum, Johann, 556 Thymine (T), 667, 667, 672, 673 Thyroid goiter in, 388b medical imaging of, 293 Thyroxine, 293, 388b, 586, 587 Time equilibrium in chemical reactions and, 229 measurement of, 11 Tincture, 397 Titration, calculating solution concentrations using, 259, 259–61, 270 acid-base titration, 260 TNT (2,4,6-trinitrotoluene), 389b Tollens’ reagent, 463 Toluene, 384 nitration of, to TNT explosive, 389b Toluidine, 444 Tools balances, 10 barometer, 143 Geiger-Müller counter, 287 hydrometer and urinometer, 20 manometer, 143, 144 pH meter, 258 polarimeter, 435 Tooth enamel solubility and decay, 127b Topoisomerases (gyrases), 683, 691 Torricelli, Evangelista (1608-1647), 143 Toxins cholera, 652 tetrodotoxin, in puffer fish, 337b Trace elements, 798t Tranquilizers, 446b Trans (prefix), 338, 346 See also Cis-trans isomers Transamination, 761 Transcription, 676, 696, 697–99 properties of mRNA during, 680 Transcriptional-level gene regulation, 710–12 at post-transcription level, 713 at transcriptional level, 710–12 Transcription factor, 658 Transcription factors, 698, 723 gene expression and role of, 710, 711, 712, 713 helix-turn-helix, and leucine zipper, 712 metal-binding fingers of transcription factors, 712 Trans fatty acids, 481b–482b Transferases, 616, 617t Transfer RNA (tRNA), 677, 678t, 691, 696 initiation of protein synthesis and role of, 703 specificity of, for unique amino acid, 714 structure of, 677 translation and role of, 700 Transition elements, 44 Transition state, 215, 216, 235 enzyme catalysts and, 623, 634 I21 ■ Index Transition-state analogs, 629, 631, 632b, 634 Translation, 676, 696–97, 723 properties of mRNA during, 680 Translational-level gene regulation, 708, 714 Translocation, elongation stage of protein synthesis, 705 Translocator inner membrane (TIM), 727 Translocator outer membrane (TOM), 727 Transmembrane channels, 554b Transmembrane protein, 644 Transmutation, 280 Transport across membranes, 552, 554b anion, 554b cholesterol, 561–63 facilitated, 554b of oxygen by hemoglobin, 606b passive transport, 554b removal of neurotransmitters by, 649 role of proteins in, 579 Transporter molecules, 649 Transuranium elements, 297 Triacylglycerols, 548 See also Triglycerides 2,4,6-Tribromophenol, 386 Tricarboxylic acid (TCA) cycle, 491 See also Citric acid cycle Trichloroacetic acid, 485 Triglycerides, 483, 547, 548 physical and chemical properties of, 548–51 structure of, 547–48 Trigonal planar, 95 2,3,4-Trihydroxybutanal, 430, 431 Trimethylamine, 315, 441, 446 Trimethylpentane, 343b Trinitrotoluene, 738b Triol, 400 Trioses, 518 Tripeptide, 589, 593 Triphosphate ion, 509 Triphosphoric acid, 509 Triple bond, 83 Triple point, 168 Tri- (prefix), 518 Triprotic acid, 244 Trisaccharides, 533 TRIS buffer, 268, 269t tRNAfMet, 703, 704 Trypsin, 615, 618, 795 regulation of, 626 Tryptophan, 582, 615, 795 T (taut) form of enzyme, 627, 627 Tumor necrosis factor (TNF), 824 Tumor suppressor genes, 717b 2G12 antibody, 836 Tyndall effect, 195, 195–96 Tyrosine, 582, 586, 587, 795 U Ubiquinone See Coenzyme Q Ulcers, 655 Ultra-extensive metabolism (UEM) of drugs, 687b Ultraviolet (UV) light, 278, 506b Universal gas constant (R), 148 Unsaturated aldehydes, 458 Unsaturated fats, 479t, 480, 548, 549t, 757 Unsaturated hydrocarbon, 324 Unsaturated solution, 181 Uracil (U), 667, 667, 687, 688 Uranium-235, 298 Urea, 508b, 615 formation of, 308, 762–64 Urea cycle, 762–64, 768 Urease, 615 Uridine, 668 Uridine diphosphate (UDP)-glucose, 776, 777 Uridine triphosphate (UTP), glucose conversation to other carbohydrates and role of, 776, 777 Urine glucose in, 530b ketone bodies in, 759 pH of, 257 Urinometer, 20 Uronic acids, oxidation of monosaccharides to, 530–31 Urushiol, 390 U.S Department of Agriculture (USDA), 789, 789 V Vaccines, 825b against HIV infection, 832, 833 Valence electrons, 55, 61 octet rule, 69–71 Valence shell, 55, 61 Valence-shell electron-pair repulsion (VSEPR) model, 92–96, 100 of alkenes, 354 of carbon compounds, 311t predicted molecular shapes based on, 96t Valine, 581 Vanillin (vanilla bean), 461b Vapor, 159 phase change from ice to water, 166–70 Vaporization, heat of, 166, 171 Vapor pressure of liquids, 158–61, 159, 171 temperature and change in, 161 Vasoconstrictors, 451b Vasopressin function, 594–95 structure, 595 Vegetable oils, fatty acids in, 479t Very-low-density lipoprotein (VLDL), 561 composition and properties of human, 562t Vesicles, neurotransmitters stored in, 642, 661 Viagra (drug), 624b, 654b Vidarabine (Vira-A) (drug), 709b Vinyl chloride, 371 Viruses, 709b antiviral therapy, 709b, 832 gene therapy using, 721–22, 722 HIV See Human immunodeficiency virus (HIV) recombinant DNA using, 719 Vision, role of cis-trans isomerism in human, 361b Vitamin(s) nutritional importance of, 797, 798t, 804–5 sources, functions, deficiencies and daily requirements of, 799t–802t Vitamin A (retinol), 361b, 363 Vitamin B, 618, 804 Vitamin C, 311, 526b, 797 Vitamin D, 797, 805 Vitamin E, 393, 797 V(J)D gene, diversity of immune response due to recombination and mutation of, 819 Voltaic cells, 131b Volume, 9–10 measurement of, 9–10 pressure and, for gases, 144, 144, 146 temperature and, for gases, 146 Von Euler, Ulf, 569 VSEPR See Valence-shell electron-pair repulsion (VSEPR) model W Warren, John, 410b Waterbeds and specific heat of water, 23b Water constant (Kw), 254 Water (H2O) acetic acid and, reaction between, 247 acid–base properties of, 253–56 ammonia and, reaction between, 227 boiling point, 162t density of, 18, 162b energies involved in phase change from ice to vapor, 166–70 formulas, 34 gas solubility in, 180t hydrochloric acid and, reaction between, 214, 247 hydrogen bonds joining molecules of, 155 hydrolysis reactions involving, 503–7 ion product of, Kw (water constant), 254 ion reactivity with, 126 Lewis structure and ball-and-stick molecules, 94 models of, 34 molecular polarity of, 98 as nutrient, 805 phase diagram for, 168 reverse osmosis and production of drinkable, 201b solubility of alcohols and alkanes in, 402t solutions with, as solvent See Aqueous solution(s) as solvent, 191–95 specific heat of, 23b Water of hydration, 191 Water-strider (insect), 158 Watson, James (1928–), 672, 673 Wavelength (l), electromagnetic radiation, 278 Waxes, 550b paraffin, 340, 340 Weak acids, 242, 245t Ka and pKa values for select, 249t Weak bases, 242t, 243, 245t Weak electrolytes, 193 Weight, defined, 10 Weight reduction in humans artificial sweeteners and, 796b–797b diets for, 788, 792, 794, 796b–797b drugs for, 738b reasons for difficulty of, 793b Wells, Horace, 410b White blood cells (leukocytes), 811, 812, 826, 836 lymphocytes as type of See Lymphocytes Wilkins, Maurice (1916–2004), 672 Wine grapes, fermentation of, 397 Wöhler, Friedrich (1800–1882), 308 X X as symbol for halogen, 44 X-rays, 278 Xylene, 385 Xylitol, 529 Y Yeast, 252 Yew, Pacific (Taxis brevifolia), production of taxol from bark of, 310b -yne (suffix), 355, 375 Z Zeno of Elea (b 450 BCE), 31–32 Zinc fingers, transcription factors, 712, 713 Zinc oxidation, 128 Zwitterions, 269t, 583, 583–84, 592, 608 Zymogens See Proenzymes (zymogens) This page intentionally left blank Some Important Organic Functional Groups Functional Group* OH Alcohol Example IUPAC (Common) Name CH3CH2OH Ethanol (Ethyl alcohol) O O C Aldehyde H Alkane Alkene Alkyne Ethanal (Acetaldehyde) CH3CH3 Ethane C C CH2 CH2 Ethene (Ethylene) C C HC CH Ethyne (Acetylene) O O Amide C Amine NH2 N O C Anhydride CH3CH O CH3CNH2 Ethanamide (Acetamide) CH3CH2NH2 Ethanamine (Ethylamine) O O O C CH3COCCH3 Ethanoic anhydride (Acetic anhydride) Benzene Arene O O Carboxylic acid C OH CH3COH Ethanoic acid (Acetic acid) Disulfide S S CH3SSCH3 Dimethyl disulfide O Ester C Ether Haloalkane (Alkyl halide) Ketone O O C CH3COCH3 Methyl ethanoate (Methyl acetate) O CH3CH2OCH2CH3 Diethyl ether X CH3CH2Cl Chloroethane (Ethyl chloride) X F, Cl, Br, I O O C CH3CCH3 OH Phenol OH Propanone (Acetone) Phenol Sulfide S CH3SCH3 Dimethyl sulfide Thiol SH CH3CH2SH Ethanethiol (Ethyl mercaptan) The Standard Genetic Code First Position (5' End) U C A G Third Position (3' End) Second Position U C A G UUU Phe UCU Ser UAU Tyr UGU Cys U UUC Phe UCC Ser UAC Tyr UGC Cys C UUA Leu UCA Ser UAA Stop UGA Stop A UUG Leu UCG Ser UAG Stop UGG Trp G CUU Leu CCU Pro CAU His CGU Arg U CUC Leu CCC Pro CAC His CGC Arg C CUA Leu CCA Pro CAA Gln CGA Arg A CUG Leu CCG Pro CAG Gln CGG Arg G AUU Ile ACU Thr AAU Asn AGU Ser U AUC Ile ACC Thr AAC Asn AGC Ser C AUA Ile ACA Thr AAA Lys AGA Arg A AUG Met* ACG Thr AAG Lys AGG Arg G GUU Val GCU Ala GAU Asp GGU Gly U GUC Val GCC Ala GAC Asp GGC Gly C GUA Val GCA Ala GAA Glu GGA Gly A GUG Val GCG Ala GAG Glu GGG Gly G *AUG forms part of the initiation signal as well as coding for internal methionine residues Names and Abbreviations of the Common Amino Acids Amino Acid Three-Letter Abbreviation One-Letter Abbreviation Alanine Ala A Arginine Arg R Asparagine Asn N Aspartic acid Asp D Cysteine Cys C Glutamine Gln Q Glutamic acid Glu E Glycine Gly G Histidine His H Isoleucine Ile I Leucine Leu L Lysine Lys K Methionine Met M Phenylalanine Phe F Proline Pro P Serine Ser S Threonine Thr T Tryptophan Trp W Tyrosine Tyr Y Valine Val V ... pentane butanal 2- butanone 1-butanol propanoic acid CH 3CH 2OCH 2CH CH 3CH 2CH 2CH 2CH CH 3CH 2CH 2CHO CH 3CH 2COCH CH 3CH 2CH 2CH 2OH CH 3CH 2COOH Boiling Point (°C) 74 72 72 72 74 74 34 36 76... stearic acid arachidic acid CH CH 2 5CHwCH CH 2 7COOH CH CH 2 7CHwCH CH 2 7COOH CH CH 2 CHwCHCH 2 CH 2 6COOH CH 3CH CHwCHCH 2 CH 2 6COOH CH CH 2 CHwCHCH 2 CH 2 2COOH palmitoleic acid oleic acid linoleic... between 12 and 20 carbon atoms are known as fatty acids We study them further in Chapter 21 16, 18, and 20 carbon atoms are particularly abundant in animal fats and vegetable oils (Section 21 .2) , and