Index I-15 substrates in, 554–558, 556F, 558B thermodynamics of, 538T Glycolytic pathway, 520 Glyconjugates, 213 Glycopeptide transpeptidase, 402F, 403 Glycophorin, 249, 249F, 252F Glycoprotein, 120, 120T, 204–209 antifreeze, 207, 207S N-linked, 205S structure of, 205S Glycosaminoglycan, 209 Glycosides cardiac, 279, 280S, 282B description of, 191 Glycosidic bond, 192, 678F Glycosphingolipid, 227, 1031 Glycosyl phosphatidylinositol, 257, 258F, 260 Glycosylceramide, 746F Glyoxylate, 656 Glyoxylate cycle, 587, 587F, 588, 589 Glyoxysome, 588F, 589, 714 Glyphosate, 801B GMK, 207B GMP, 814, 815F, 816–818, 820F GMP synthetase, 819 Gold, fool’s, 583B Golgi apparatus, 20 of animal cell, 23T of plant cell, 24T Gout, 824–825 GPCR signal, 1024–1025 GPI, 260 G-protein-coupled receptor, 251, 1013, 1015, 1037–1043 GPT, 668–669 G-quadruplexes, 329, 330F Gradient concentration, 270 ion, in neuron, 1044 proton, 611–620, 614F, 616F, 617F, 618F, 619B, 619F flagella and, 503–504 Gradient separation of amino acids, 86F Gram-negative bacteria, 201, 202S, 203 F Gram-positive bacteria, 201, 202S, 203F, 204 Granule, storage, 20T Granum, thylakoid, 631 Grass, 656 Gratuitous inducer, 914D GRE, 928 Green fluorescent protein, 81B, 81G, 372 GroEL chaperonin, 168 GroES–GroEL complex, 990–992, 992F, 992G Groove, major or minor, 322 Group, prosthetic, 598 Group transfer potential, 58–59, 59T Growth, 839–840 Growth factor, 212, 829B Growth factor receptor , 1016 Growth hormone, 1009F GTP hydrolysis, 972 of phosphoric acid anhydrides and, 59–60 in protein synthesis, 972 in TCA cycle, 576 GTPase-activating proteins, 1038F GTP-binding protein, 466 G:U base pair, 958 Guanidino group, 785 Guanine, 292, 293S Guanine deaminase, 823 Guanine-nucleotide exchange factor, 969 Guanosine, 295, 295S Guanosine 5Ј-diphosphate, 296 Guanosine 5Ј-monophosphate, 295, 296S Guanylic acid, 295 Guanylin, 1021 Guanylyl cyclase, 1015, 1021, 1024 Guanylyl transferase, 940 Guide strand, 375 Guncotton, 201B Gyrase, DNA, 334–335, 335F H bond. See also Hydrogen bond description of, 321 with polar solutes, 31 in water, 29–30, 30F of water, 45 H zone, 483 Hairpin, 166 Half-cell, 594 Halobacterium halobium, 250 Halorhodopsin, 285 Handedness of peptide bond, 138B Hanes–Woolf plot, 272F, 395, 396F Hatch–Slack pathway, 656–659 HATs, 933 Haworth, Sir Norman, 185 Haworth projection, 185–187, 185S, 186S H-chain gene, 899–900 HDACs, 934 HDL, 757 H-DNA, 329 H ϩ /2e Ϫ ratio, 611 Heart cardiac glycosides and, 279, 280S, 282B energy metabolism of, 848T metabolic role of, 848F, 851 Heart myocyte, 204 Heat, endogenous uncouplers and, 618, 619B Heat capacity, 56 Heat denaturation of DNA, 331F Heat shock protein, 168, 988 Heat shock transcription factor, 929 Heating of water, 44–45 Heat-stable enterotoxin, 1021 Heavy chain, 484 Heavy isotope, 526 ␣-Helical barrel, 256 Helical twist, 323F Helical wheel, 153, 1033, 1033F Helicase, 481, 498, 499T, 863 Helix ␣-, 95F, 137, 139–142, 936 amphipathic, 997 basic amphiphilic, 1033 from calmodulin, 154G from citrate synthase, 154G from flavodoxin, 154G in proteins, 137, 139–142, 140F, 141F transmembrane, 251 amphiphilic, 153 Baa, 1033 double, 299–303, 300F, 301S antiparallel nature of, 300F Chargaff’s analysis of, 300 digital encoding of, 302 as dynamic structure, 326–327, 327F as stable structure, 321–323, 322F, 323F Watson–Crick postulate of, 301, 301F in globular proteins, 152–153, 152F, 152G, 154G hydrogen bond and, 140F unwinding of, 863 Helix 2, 936 Helix behavior of amino acids, 142T Helix capping, 141F, 142 Helix-turn-helix, 936 Hellin g, Robert, 358 Heme, 467D, 607–608 Heme iron, 471, 473, 473B Heme protein, oxygen-binding, 113 Hemiacetal, 184, 191S Hemicellulose, 532 Hemiketal, 184, 186S, 191S Hemoglobin, 467–468 -, 141F 2,3-bisphosphoglycerate and, 475, 475F, 476F carbon dioxide and, 474–475 ␣-chain, 113 -chain, 113 dimers of, 469F fetal, 475–476 heme iron and, 471, 473 myoglobin compared with, 467–469, 468F, 468S nitric oxide and, 477 B oxy and deoxy forms of, 473 oxygen binding of, 468F, 469–471 pathological sequence variants of, 117T proteins of, 113, 115F quaternar y structure of, 469, 471 salt bridges between subunits of, 473F structure of, 96F, 113, 468S subunit motion of, 472F tetrameric structure of, 469 Hemoglobin:oxygen interaction, 472B Hemolymph, 193B Hemopexin C-terminal domain, 169F Hemoproteins, 120T Henderson–Hasselbalch equation, 38, 77 Heparin, 200–201, 200S, 211S HEPES, 44S Heptad repeat pattern, 148B Heptulose, 183 Herbicide, 801B Hereditary emphysema, 172B Heredity, 862D directing changes in, 375, 377, 378B, 379 Heterochromatin protein 1, 934 Heterogeneous nuclear RNA, 303, 940 Heterologous probe, 363 Heterologous protein subunit, 173, 174F Heteromultimer, 101, 173 Heteromultimeric protein, 89D Heteropolysaccharide, 194 Heterotroph, 511D Hevamine, 169F I-16 Index Hexokinase, 116F, 539–541, 540F in chemical reaction, 420T size of molecule, 90T Hexose Calvin–Benson cycle and, 653, 655 synthesis of, 647–648 Hexulose, 183 HGPRT, 821, 822B High-density lipoprotein, 757 High-energy biomolecule, 57–63 High-energy bond, 58 High-energy bond transfer potential, 59T High-energy phosphate compound, 57, 57T High-performance liquid chromatography, 86, 132 High-pressure liquid chromatography, 99 High-spin state, 473B High-throughput DNA sequencing, 319B Histamine, 75S, 76 Histidine, 549F, 803F evolution and, 806B pK a value for, 77T structure of, 73S synthesis of, 802, 803F Histidine–imidazole group, 42 Histone, 302, 336, 336T, 933–934 Histone code, 933–934 Histone deacetylase complex, 934 HIV infection, 443B, 876B HIV mRNA, 442F HIV-1 protease AIDS drugs and, 443B characteristics of, 441–442 with inhibitor, 442G pH-rate profile for, 440F structure of, 440G HIV reverse transcriptase, 877 H ϩ ,K ϩ -ATPase, gastric, 280–282, 282F HMG-CoA lyase, 718 HMG-CoA reductase, 752, 752F, 754F HMG-CoA synthase, 751–752 hnRNA, 303, 305 Holliday junction, 883F, 883G Holliday model, 878–880, 879F Holoenzyme, 385 E. coli polymerase III, 867–868, 867T Homeobox domain, 936 Homeostasis, 16, 847D Homodimer, 89D glycogen phosphorylase as, 462–463 Homodisaccharide, 192 Homogentisate dioxygenase, 810B Homoglycan, 194 Homologous protein, 111 Homologous recombination, 877 Homolytic cleavage, 711 Homomultimer, 173 Homomultimeric protein, 89D Homopolysaccharide, 194 Homoserine acyltransferase, 790 Homoserine dehydrogenase, 790 Homoserine kinase, 790 Honey, 190B Hoogsteen base pairs, 328–329 Hop diffusion, 265 Hormone adenylyl cyclase and, 465F adrenocorticotropic, 763 definition of, 1008D eating behavior and, 853–854 eicosanoids as, 747 fatty acid release and, 697, 700–701 fatty acid synthesis regulated by, 737, 738F glycogen synthesis regulated by, 680–683, 680F ␣-melanocyte stimulating, 854 polypeptide, 1010 signal-transducing receptors responding to, 1012F, 1013–1024, 1013F, 1013G, 1024B steroid, 233, 234S, 1008–1009, 1008D Hormone-activated enzyme cascade, 465F Hsp, 988 Hsp60 chaperone, 168, 988–989, 989F HTH motif, 936 HtrA protease, 1003 Huber, Robert, 642 Human bactericidal permeability-increas- ing protein, 169F Human body, composition of, 5T Human genome, 121F, 367B, 425B Human growth hormone, 169F Human growth hormone gene, 889B Human immunodeficiency virus infection, 443B, 876B Huntington’s disease, 988B Hyaluronate, 200S, 201, 212F Hyaluronic acid-binding domain, 213 Hyatt, Isaiah, 201B Hyatt, John, 201B Hybrid duplex, 332 Hybrid protein, 371F Hybridization nucleic acid, 332–333 screening of genomic library by, 362F Southern, 362–363, 364B Hybridization experiment, colony, 362 Hydration, 30–31, 31F Hydride ion, 522 Hydrocarbon chain in membrane bilayer, 247 Hydrogen abundance of, 4 in catabolism, 522S Hydrogen bond, 11T, 12–14, 13S helix structure and, 140F low barrier , 431–432, 432F in parallel pleated sheets, 143 in peptide groups, 139F in proteins, 134–135 in water, 29–30 Hydrogen ion, 34 in dissociation of oxygen from hemoglo- bin, 473–475 secondary active transport and, 286 Hydrogen tunneling, 433 B Hydrogenase activity, 773F Hydrolysis acid, 99 of ATP to ADP, 62F equilibria in, 63–64 myosin and, 488–490 entropy factors from, 60 GTP, 972 of nucleic acids, 307–313 of phosphoric acid anhydrides, 59–60 of starch, 673F Hydronium ion, 34 Hydropathy index, 251 Hydropathy plot, 251, 252F Hydrophobic collapse, 162 Hydrophobic core, 167D Hydrophobic effect, 146 Hydrophobic interaction, 9, 11T, 13–14, 31–33, 135 Hydrophobic interaction chromatography, 132 Hydrophobic protein in bacterial cell wall, 203 L-Hydroxy-acyl-CoA dehydrogenase, 706–707 Hydroxyapatite, 151 -Hydroxybutyrate, 849S -Hydroxybutyrate dehydrogenase, 718 7␣-Hydroxycholesterol, 761F -Hydroxydecanoyl thioester dehydrase, 734 Hydroxyeicosanoic acid, 747 Hydroxyethyl-TPP, 567, 571F -Hydroxyl group, 706–707 Hydroxyl ion, 34 7␣-Hydroxylase, 762 Hydroxylase factor-inhibiting hypoxia inducible factor, 559 Hydroxylated residue of collagen, 150F of proline, 150S Hydroxylysine, 75S, 76 p-Hydroxyphenylpyruvate dioxygenase, 809 17-␣-Hydroxyprogesterone, 238S Hydroxyproline, 75S, 76, 150S Hydroxyprolyl residue, 150F 17--Hydroxysteroid dehydrogenase, 238S 17--Hydroxysteroid dehydrogenase 3 defi- ciency, 238S Hypercholesterolemia, familial, 760–761 Hyperchromic shift, 330 Hyperpolarization, 1053 Hyperuricemia, 825 Hyperventilation, 44B Hypothesis lock-and-key, 409–410 Mitchell’s chemiosmotic, 609 operon, 914 wobble, of codon–anticodon pairing, 959 Hypoventilation, 44B Hypoxanthine, 293S Hypoxanthine-guanine phosphoribosyl- transferase, 821 Hypoxia inducible factor, 559 Hypoxia inducible factor-1, 559 Hypoxia inducible factor-1␣, 559 I band, 483 Ibuprofen, 751S Ice, 29–30, 29F Identical subunit dimer of, 441 protein, 173, 176F D-Idose, 182S L-Iduronic acid, 188S IFs, 967 Imidazole p-nitrophenylacetate hydrolysis by, 431F titration curve for, 40, 41F Index I-17 Immunodeficiency syndrome, severe com- bined, 378B, 822B Immunoglobulin, 176F, 177B, 413, 897, 898F Immunoglobulin fold, 897 Immunoglobulin gene, 897, 899, 902 Immunoglobulin module, 156F Immunology, 895, 897–902, 898F, 900F, 901F Immunoprecipitation, 373 IMP, 814, 815F, 816–818, 819F IMP cyclohydrolase, 817 IMP dehydrogenase, 819 In vitro mutagenesis, 374–375 Inanimate environment, nitrogen in, 768–769 Indinavir, 443S Indirect readout, 937 Indole-3-glycerol phosphate synthase, 802 Induced dipoles, 13 Induced fit, 409–410 Inducer, 914D Inducible operon, 918 Induction, 452, 913 Inflammation, 215 Infrared region, 82 Inhibition allosteric, 457 of enzymes, 398–403, 398T, 399B, 399F, 400F, 401F, 402F Inhibitor amino acid biosynthesis, 801B ATP synthase, 618 of citrate synthase, 572 of enzyme activity, 386, 398–403, 398T, 399B, 399F, 400F, 401F, 402F gluconeogenesis, 668B of glycogen phosphorylase, 464 HIV-1 protease, 442G mechanism-based, 834B monoamine oxidase, 1054B of oxidative phosphorylation, 616–618 protein synthesis, 981–984, 982T Inhibitory neurotransmitter, 1053 Initiation peptide chain, 965, 966–968 in eukaryotes, 976–979, 977F of transcription, 931F, 931G Initiation factor, 966, 967 eIF-4G, 978 eukaryotic, 976–977, 978T general transcription, 930T Initiator aminoacyl-tRNA, 965 Initiator tRNA, 966 Inner mitochondrial membrane translo- con, 998 Inorganic nitrogen, 768–774, 769F, 770F, 771F, 772F, 773F Inorganic precursor, 8F Inosine, 295S, 305S Inosinic acid, 814, 815F, 816–818, 819F Inositol-1,4,5-trisphosphate, 235, 1029 Insect butter fly, 282B chitin of, 190 pest control and, 257B trehalose of, 193B Insertion mutation, 893 Insertion sequence, 886 Insulin, 454, 1009F eating behavior and, 855 glycogen synthesis and, 680–681 as polypeptide hormone, 1010 size of molecule, 90T structure of, 100S Insulin receptor, 1016, 1020 Insulin receptor substrate, 1020 Insulin-like growth factor 1, 1042 Integral membrane protein, 249F, 251–256, 255F, 270 R. viridis photosynthetic reaction center as, 642 Integral protein, 246 Inteins, 896B Interaction DNA:protein, 922 electrostatic, 321 hemoglobin:oxygen, 472B hydrophobic, 9, 13–14, 31–33, 135 ionic, 13 molecular, in water, 30 noncovalent, in proteins, 134–136 protein-protein, 922–923 van der Waals, DNA and, 321–322 Interaction energy, van der Waals, 12F Intercalating agent, 326 Intercalation, 893 Intermediate acyl carrier proteins and, 727 acyl-enzyme, 436 amphibolic, 520 2-carboxy-3-keto-arabinitol as, 651 lariat, 942 metabolic integration and, 840 resonance-stabilized carbanion, 711F transition state vs., 419 tricarboxylic acid cycle providing, 581–582, 581F Intermediate-density lipoprotein, 757 Intermembrane space, 592 Internal energy, 48–49 Internal loop, 343 International unit, 393D Intervening sequences, 303 Intestine, small, fatty acids in, 699F Intolerance, lactose, 557, 558B Intracellular buffering system, 42 Intracellular calcium-binding protein, 1031, 1033 Intracellular nucleotidase, purine catabo- lism and, 823 Intracellular second messenger, 1026T Intramolecular ionic bond, 14S Intramolecular tunnels, 802B Intrasteric control, 460 Intrastrand base pairing, 342, 344–345, 346, 348 Intrinsic binding energy, 421, 421F Intrinsic coagulation pathway, 455 Intrinsic protein, 246 Intrinsic termination, 912 Intrinsically unstructured protein, 168, 170F Intron, 303, 939 Invariant residues, 113 Invertase, 193 Inverted repeat, 327, 328F Invirase, 443S Ion, 13 hydride, 522 hydrogen, 34 hydronium, 34 hydroxyl, 34 magnesium, 656 metal, 432–433 salt, 98 secondary active transport and, 286 Ion channel ligand-gated, 1047 oligomeric, 1047 voltage-gated, 1044 Ion exchange chromatography, 85–86, 127–128 Ion gradient in neuron, 1044 Ion product of water, 35 Ionic bond, 14F Ionic interaction, 11T, 13 Ionization of amino acid side chains, 78–79 entropy factors from, 60 stabilization of hydrolysis products by, 60 of water, 34–35, 34F Ionization constant, 37 IP 3 , 1032F IPTG, 914, 914F Iron, heme, 471, 473, 473B Iron–sulfur cluster, 573, 573F Iron–sulfur protein, 598 Irreversible enzyme inhibition, 401–403 Islets of Langerhans, 680 Isoacceptor tRNA, 959 Isocaproic aldehyde, 238S Isocitrate citrate and aconitase and, 572–573 in tricarboxylic acid cycle, 572–574 Isocitrate dehydrogenase electron transport and, 574 regulation of, 586 in tricarboxylic acid cycle, 574, 574F, 574G Isocitrate lyase, 587–588, 588F Isoelectric focusing, 131 Isoelectric point, 97 Isoform, protein, 944 Isolated system, 48, 49F Isolation of cloned fusion proteins, 371T protein, 97–98 Isoleucine catabolism of, 807, 808F pK a value for, 77T stereoisomers of, 83B structure of, 73S synthesis of, 790, 793, 794F Isologous protein subunit, 173, 174F Isomaltose, 192, 192S, 196 Isomerase in beta-oxidation of fatty acids, 713–714 triose phosphate, 544, 545F, 545G Isomerization of citrate by aconitase, 572–573 of glucose-6-phosphate, 541 Isopentenyl pyrophosphate, 753 Isoprene, 229, 230S plants emitting, 231B Isopropyl -thiogalactoside, 914, 914F Isopropylmalate dehydratase, 793 I-18 Index Isopropylmalate dehydrogenase, 793 Isopropylmalate synthase, 793 Isopycnic centrifugation, 332B Isoschizomer, 312 Isotopic tracer, as metabolic probe, 525–526, 525T, 526F Isozyme, protein kinase C as, 1035–1036 IUP, 168 Janus protein kinase, 1037 Jeffery, Constance, 543B JH gene, 900 Judson, Horace Freeland, 143B Junction, 343, 343F Holliday, 878–880, 879F synaptic, 1052 Juvenile hormone esterase, 425B K a , 36–37 Kappa gene family, 899 k cat , 393, 393T k cat /K m ratio, 393–394 KcsA, 274 K eq , ATP changing, 67B Keratan sulfate, 200S, 201 Keratin ␣-, 147, 147F, 149 -, 149 Ketal, 191, 191S ␣-Keto acid, 780S -Ketoacyl-CoA intermediate, 707 Keto-enol tautomeric shift, 293 Ketogenesis, 717D Ketogenic amino acid, 531 Ketogenic intermediate, 804 ␣-Ketoglutarate, 150S, 806 ␣-Ketoglutarate dehydrogenase, 575, 575T ␣-Ketoglutarate family of amino acids, 781B, 781T, 783–787, 783F, 784F–786F, 787B Ketohexose, 183, 183S Ketone, 186S, 532B Ketone body, 717–718, 717B, 718F Ketopentose, 183, 183S Ketose, 183, 183S 3-Ketosphinganine reductase, 744 3-Ketosphinganine synthase, 745 Ketotetrose, 183, 183S -Ketothiolase, 707, 751 Ketotriose, 183S Kidney, gluconeogenesis in, 662–663 Kilocalorie, 49 Kinase homoserine, 790 mitogen-activated protein, 1034B nucleoside diphosphate, 666 pyruvate dehydrogenase, re gulation of, 584–586 receptor tyrosine, 1016–1017, 1030, 1030F ribulose-5-phosphate, 653 triose, 555 tyrosine, 1015–1016 Kinesins, 481, 492, 495–496, 497F Kinetics burst, 436F chemical, 386 definition of, 386 of enzyme-catalyzed reaction, 403–409, 403F, 405F, 406F, 406S ping-pong, in fatty acid synthesis, 724 zero-order, 389 K m , 391D, 394T KNF model, 458 Knob, synaptic, 1044 Knockout mice, 884B Knoop, Franz, 701–702 Koshland–Nemthy–Filmer sequential model, 473 Krebs, Hans, 563 Krebs cycle, 563–591. See also Tricarboxylic acid cycle K w , 35 Label, affinity, 402 lac operon, 914F, 914–915 lac repressor, 915, 915F, 917B, 917T ␣-Lactalbumin, 116, 116G -Lactamase, k cat /K m ratio of, 394T Lactase, 193 Lactate gluconeogenesis and, 662, 669 pyruvate metabolism and, 552–553, 553F Lactic acidosis, 681B Lactic dehydrogenase, 455–456, 456F - D-Lactose, 193 Lactose intolerance, 557 Lactose synthase, 558B Lagging strand in DNA replication, 864 LamB protein, 255 Lambda gene family, 899 Lambda receptor, 255 Lamella, 19, 631 Landscape, energy, 163 Langdon, Robert, 753B Lanolin, 229 Lanosterol, 230S, 231, 757 Lariat intermediate, 942 Lathyrism, 155B ␣-Latrotoxin, 1047 Lauric acid, 220T Laws of thermodynamics, 48–52 LCAT, 758 L-chain gene, 899 LDL, 206, 757, 758, 760–761 L-dopa, 1056 Leader peptidase, 994 Leader peptide, 921F, 994 Leading strand in DNA replication, 864 Leading substrate, 405 Learning, 936B Lecithin, 225 Lecithin:cholesterol acyltransferase, 758 Lectins, 213, 213T Left-handed DNA, 323–324, 325F, 326 Leloir pathway, 556–557 Leptin, 855 Lesch-Nyhan syndrome, 822B Lethal synthesis, 834B Leucine catabolism of, 807, 808F pK a value for, 77T structure of, 72S synthesis of, 793, 795F Leucine aminotransferase, 793 Leucine zipper-basic region, 936 Leukemia, 789B Leukemia virus, Maloney murine, 377 Leukosialin, 206 Leukotriene, 747 Levinthal’s paradox, 162 Levorotatory behavior, 80 Library, DNA. See DNA library Life cell as unit of, 9 time scale of, 17T Life cycle, ribosome, 976F Ligand-binding site, 122–123 Ligand-gated ion channel, 1047 Ligand-induced conformational changes, 123 Ligase Acyl-CoA, 702 DNA, 869 phage T4 DNA, 357 ubiquitin-protein, 998 Light, ultraviolet amino acid absorbing, 82, 92 denaturation of DNA and, 330–331 pyrimidine dimer repair and, 890 pyrimidines and purines and, 293, 293F Light activation, 655 Light chain, 484, 484F Light energy chlorophyll capturing, 633–634, 634F, 634S, 635F, 635S, 636–637, 636F in membrane transport, 285, 285F Light reaction, photosynthetic, 632, 632F Light regulation of carbon dioxide fixation, 655–656, 655F Light-driven ATP synthesis, 648–650, 649F, 650F Light-harvestin g complex, 637, 647 Light-harvesting pigment, 634, 635S Light-induced change in chloroplast com- partment, 655, 655F Lignin, 532, 798 Lignoceric acid, 220T Limit dextrin, 674 Limonene, 230S Linear molecular motor, 481 Lineweaver–Burk plot, 272F, 395 of competitive inhibition, 399F of mixed noncompetitive inhibition, 401F nonlinear, 395 of uncompetitive inhibition, 402F Link protein, 213 Linker, 357 Linking number, 334 Linoleic acid, 220T, 221G, 221S 1-Linoleoyl-2-palmitoylphosphatidylcholine, 226 Lipase, 758 Lipid, 219–241. See also Lipid biosynthesis as biological signals, 234–237 fatty acids, 219–222, 220T, 221G, 221S. See also Fatty acid entries glycerophospholipids, 223G, 223S–225S, 225F, 226F, 227B membrane proteins anchored in, 256–257 movements of, in membranes, 261–269 nutritional, 531 Index I-19 sphingolipids, 227–229, 228F spontaneously formed structures of, 244–245, 244F, 245S steroids, 233, 234F, 234S, 236B, 238S terpenes, 229–232, 230S, 231B, 231S, 232B triacylglycerols, 222, 222G, 222S, 223 waxes and, 229, 229B, 230S Lipid biosynthesis, 722–767 bile acids and, 761–762, 761F of complex lipids, 737–747 CDP-diacylglycerol and, 740F, 741–743 ceramide and, 746–747 glycerolipids and, 738–741 phosphatidylethanolamine, 741, 741F platelet-activating factor and, 744, 744F sphingolipid and, 744–745 fatty acid, 722–737. See also Fatty acid synthesis steroid hormones and, 762–764 Lipid transverse asymmetry, 260 Lipid-anchored proteins, 248 Lipidomics, 237–238 Lipoic acid, 524T, 570B Lipopolysaccharide, 203, 203F Lipoprotein, 120T, 206, 757T–759T, 758, 758G, 760–761 Lipoprotein complex, 757 Lipoprotein lipase, 758 Liposome, 245 Liquid-disordered state, 263, 265 Lithium, 1031B Liver cortisol and, 684F energy metabolism of, 848T energy stored in, 698T gluconeogenesis in, 662–663 glucose in, 669 metabolic role of, 848F, 852–853, 853 F pentose phosphate pathway and, 684 Liver alcohol dehydrogenase, 173G Living organism, 1 Living system, 1–4 Lock-and-key model, 409–410 Long-chain acyl-CoA dehydrogenase, 705 Long-term memory, 936B Loop anticodon, 953 extra, 345 internal, 343 reactive-center, 171B variable, 345 ␣-Loop, 167 Looping, DNA, 923 Loops, 343F Lovastatin, 755B Low barrier hydrogen bond, 431–432, 432F Low-density lipoprotein, 206, 757, 758, 760–761 Low-spin state, 473B Lumen, thylakoid, 631 Luteinizing hormone, 1009F L yase ATP-citrate, 724 HMG-CoA, 718 Lycopene, 230S Lymphocyte homing receptor, 212 Lysine catabolism of, 809 pK a value for, 77T structure of, 73S synthesis of, 785, 786F, 787, 788F, 790, 791F titration of, 79F Lysine residue, 285S Lysis, cell, 22 Lysogeny, 22 Lysophosphatidic acid, 235 Lysosomal acid lipase, 758 Lysosome, 20, 23T Lysozyme, 90T, 116, 116G M disc, 483 M line, 483 Macrolides, 982 Macromolecular synthesis, 839–840 Macromolecule, 1, 8F architecture of, 10, 11, 11G information in, 10–11 metabolites and, 5–7 Macrophage, 897 Magnesium ion ATP hydrolysis and, 64–65 thylakoid vesicles and, 656 Major groove, 322 Malaria, 835B L-Malate, 577S, 579B Malate dehydrogenase, 578, 657 Malate synthase, 587, 587F, 588 Malate–aspartate shuttle, 621 Malathion, 1051S, 1052 MALDI-TOF mass spectrometry, 106T Malic enzyme, 713F Malignancy. See Cancer Maloney murine leukemia virus, 377 Malonyl-CoA, 722 Malonyl-CoA–acetyl-CoA-ACP transacylase, 729 Maltase, 193 Maltoporin, 254F–255F, 255, 255F, 258F Maltose, 192, 192S, 408 Mammal CPS-II activation in, 829B polyunsaturated fatty acids and, 735 Manipulation, genomic, 884B Mannan, 198S Mannitol, 189 Mannose, 556 D-Mannose, 182S Mannose-specific agglutinin, 169F ␣-Mannosyl-serine, 205S Map, metabolic, 513, 514F–515F MAP kinase, 829B MAPKs, 1034B Maple syrup urine disease, 808–809 Mapping, restriction, 312F Marfan’s syndrome, 155B Marker, selectable, 355 Mass spectrometry, 105–109, 106T, 107F–108F, 109F Mathematically defined enzyme-catalyzed reaction, 386–389 Matrix cytosol and, 600–601 definition of, 593D mitochondrial, 593 Matrix proteoglycan, cartilage, 212F Matrix-assisted laser desorption ionization- time of flight mass spectrometry, 106T MCM protein, 872 Mechanical work, 49 Mechanism-based inhibitor, 834B Mechanosensation, 267 Mechanotransduction, 267 MED proteins, 930 Mediated decay system, nonsense, 946 Mediator, 929, 930–932, 931F Medium-chain acyl-CoA dehydrogenase, 705 Megasynthases, 730 ␣-Melanocyte stimulating hormone, 854 Melting, 45 Melting temperature, 331 Melville, Herman, 229B Membrane, 242–290 cell, 9, 19, 20T, 23T curvature of, 265–266, 266F depolarized, 1044 electron transport in, 592–593 fluid mosaic model of, 245–247, 246F lateral diffusion, 265 lipids in water and, 244–245, 244F, 245S mitochondrial, 702–703 outer, 592 phase transitions of, 277 plasma, 19 proteins of, 248–260. See also Protein, membrane thylakoid, 631 transport across, 260, 269–287 energy input in, 277–285, 279F, 279 G, 282B, 282F light energy in, 285, 285F passive diffusion and, 271, 272F Membrane channels, 273T Membrane protein, 93, 94F, 251, 995 Membrane raft, 264F, 265 Membrane thickness, 246 Membrane-associated allosteric enzyme, 1016–1017 Membrane-bound systems, 516 Membrane-spanning supramolecular com- plex, 638 Memory, long-term, 936B Menthol, 230S Meperidine, 617S -Mercaptoethylamine, 570B Meselson–Weigle experiment, 878F Mesosome, 19 Messenger , second cyclic AMP as, 1025–1026, 1026F, 1026G, 1026T intracellular, 1026T released by phospholipase, 1028 Messenger RNA. See mRNA entries Metabolic channeling, 828–829 Metabolic experiment, isotopic tracers in, 525–526, 525T, 526F Metabolic fuel, stored, 698T I-20 Index Metabolic integration anabolism and, 839 ATP coupling and, 841–843 catabolism and, 839 intermediates and, 840 macromolecular synthesis and, 839–840 in multicellular organism, 847, 848F, 848T, 849–853, 851B, 851F photochemical apparatus and, 841 quantification of cellular energy and, 843–844, 844F Metabolic map, 513, 514F–515F Metabolic pathway compartmentalization of, 527, 528F, 529F for inorganic nitrogen, 768–774, 769F, 770F, 771F, 772F, 773F Metabolic probe, 525–527, 525T, 526F Metabolic regulation, 16. See also Regulation Metabolic syndrome, 708B Metabolic water, 710 Metabolism, 511–534. See also Metabolic entries ammonium and, 774–776, 775F, 776F anabolic, 518–523 catabolic, 517–520 cellular, 15, 16F classification related to, 512T diversity of, 511 flow of energy and, 512 glycogen regulating, 674–675, 675F, 678–683, 680F map of, 513, 514F–515F mutations affecting, 525, 525F NADH and, 552–553, 553F nutrition and, 531–532. See also Nutrition oxygen and, 511 pathways of, in cells, 527, 528 F, 529F pyruvate and, 552–553, 553F Metabolite, 8F in compartmentalized pyruvate carboxy- lase, 666 in erythrocytes, 539T macromolecules and, 5–7 Metabolome, 529 Metabolomics, 529 Metabolon, 517D Metal activated enzyme, 432 Metal ion, in ATP hydrolysis, 64–65 Metal ion catalysis, 432–433 Metal-activated proteins, 120T Metalloenzyme, 432 Metalloprotein, 120T, 771 Metallothionein gene, 929, 929F Meteorite, Murchison, 83B Metformin, 847 Methanogen, 19 Methemoglobin, 115F Methionine, 790 catabolism of, 807, 808F pK a value for, 77T structure of, 73S, 75 synthesis of, 790, 791F Methionyl-tRNA i fMet formyltransferase, 966 Methyl carbon, 580F Methylated base, 304 Methylation, 461T, 940 cytosine, 326 in histone code, 934 Methyl- D-glucoside, 191S Methyl-directed pathway, 889B Methylmalonyl-CoA mutase, 711 Mevalonate, 751–752, 753, 754F Mevinolin, 755B Mevinolinic acid, 755B Meyerhof, O., 535 Mg 2ϩ channel, 276 Mice fat-free, 851B knockout, 884B transgenic, 889B Micelle, 33, 33F, 244, 244F Michaelis constant, 391 Michaelis–Menten equation, 390–395, 390F, 393T–394T myoglobin and, 467 Michel, Hartmut, 642 Micro RNA, 306 Microarray, DNA, 367–368 Microtubule, 177F, 490–498, 491F, 494B Microtubule-binding protein tau, 988B Migration branch, 879, 882 electrophoretic, 316–317 Migratory bird, 709–710 Milk, lactose in, 557, 558B Mimicry, molecular, 973B Mineralocorticoid, 764 Miniband unit, 337 Minor groove, 322 Minus end of microtubule, 490 Mismatch DNA repair, 887, 889B Mitchell, Peter, 609 Mitchell’s chemiosmotic hypothesis, 609 Mitochondria, 21F of animal cell, 23T apoptosis and, 624–626 ATP–ADP translocase and, 618, 619F electron transport and, 620 of eukaryotic cell, 20 fatty acyl group crossing, 702–703 function of, 8 glyoxysomes and, 589 of plant cell, 24T in specific compartments, 592–593 Mitochondrial cytochrome c, 606F Mitochondrial disease, 582B Mitochondrial F 1 F 0 –ATP synthase, 648–649 Mitochondrial inner membrane, 610F Mitochondrial matrix, 593 Mitochondrial outer membrane translocon, 997 Mitochondrial preprotein, 997F Mitochondrial protein, 997–998 Mitochondrion, 593F Mitogen, 829B Mitogen-activated protein kinase, 829B, 1034B Mitosis, 20 Mixed noncompetitive inhibition, 400–401 Mixed-function oxidase, 762 Mobile electron carrier, 606 Mobile element, 886 MoCo, 769 Model chromosome, 338F fluid mosaic, 245–247 Holliday, 878–880, 879F Koshland–Nemethy–Filmer, 473 for light absorption by chlorophyll, 636F lock-and-key, 409–410 of Rhodopseudomonas viridis, 642F sliding filament, 486, 488–489 Modification allosteric regulation and, 462–467, 462S, 463F, 464F, 465F, 465S post-translational, 993 Module immunoglobulin, 156F protein, 1043 MoFe-protein, 771 Molar ratios of nucleic acids, 300T Molecular activity, 393 Molecular basis of mutation, 891–893, 892F–893F, 894F Molecular chaperone, 168, 988, 988D Hsp70, 988–989, 989F Molecular disease Duchenne muscular dystrophy, 486B sickle cell anemia, 476–478 Molecular interaction in water, 30 Molecular mimicry, 973B Molecular motor, 490–510 definition of, 481D flagella and, 503–504 microtubules and, 490–498, 491F, 494B muscle contraction and, 481–490. See also Muscle contraction Molecular tweezers, 489B Molecularity of reaction, 386 Molecule amphipathic, 33 amphiphilic, 33, 33F chiral, amino acids as, 70 immunoglobulin, 176 F optically active, 82B organic, in photosynthesis, 650–656, 651F, 651G, 653T, 654F, 655F recombinant DNA, 354. See also Recombinant DNA Molten globule, 162 Molybdenum cofactor, 769 Monarch butterfly, 282B Monitoring, glucose, 663 B Monoamine oxidase, 1054B Monoamine oxidase inhibitor , 1054B Monocyte, 749 Monod, Jacques, 457 Monolayer, lipid, 244, 244F Monomeric protein, 89D Monosaccharide, 182–191, 183S classification of, 182S, 183 derivative forms of, 187–191, 188F, 189F, 191F Monoterpene, 229 Monounsaturated fatty acid, 219D Motion in globular proteins, 165–166, 165T Motor, molecular, 490–510 definition of, 481D flagella and, 503–504 microtubules and, 490–498, 491F, 494B muscle contraction and, 481–490. See also Muscle contraction Index I-21 Motor neuron, 1044F Motor proteins, 481, 492–497 Mouse fat-free, 851B knockout, 884B transgenic, 889B Movement, capillary, 45 MRE, 928 mRNA, 299, 303 cDNA libraries prepared from, 363, 366 HIV, 442F 3Ј-polyadenylation of, 941 post-transcriptional processing of, 940–941 recognition and alignment of, 967 single polycistronic, 912–913 translation in protein synthesis, 965–976, 965F aminoacyl-tRNA binding in, 969–972, 970F, 973B elongation cycle in, 968, 969T GTP hydrolysis in, 972 peptide chain initiation in, 966–968, 966F, 967F, 969T peptide chain termination in, 974, 975F polyribosomes in, 976 ribosomal subunits in, 974, 976F Mucin, 206 Multicellular organism, 847, 848F, 848T, 849–853, 851B, 851F Multidrug resistance, 283, 285 Multienzyme system, 517F Multifunctional polypeptide in pyrimidine synthesis, 828 Multilamellar vesicle, 244F, 245 Multimeric proteins, 175F Multiple codons, 921 Multiplexes, 328–329 Multisubstrate reaction, 409 MurA, 169F Muramic acid, 190, 191S Murchison meteorite, 83B Murein, 201 Murine leukemia virus, 377 Muscarinic receptor, 1047, 1050–1052 Muscle energy metabolism of, 848T energy stored in, 698T lactate in, 669 metabolic role of, 848F, 849–851, 850B troponin T isoform of, 943 Muscle contraction, 481–490 actin and myosin in, 481, 483, 484F calcium ion release in, 481, 483 coiled coils in, 485, 485F conformational change in, 497–498 myosin in, 485F sliding filaments in, 486, 487F, 488–490 Muscle fiber, 489B Muscle glycogen phosphorylase, 463 Muscular dystrophy, 486B Mutagen, chemical, 893, 894F Mutagenesis PCR-based, 375F in vitro, 374–375, 375F Mutant form of human sulfite oxidase, 396B Mutant protein, 117, 171B Mutation metabolism affected by, 525, 525F molecular basis of, 891–893, 892F–893F, 894F prenyl transferase and, 259B MWC model, 457 Myocyte, heart, 204 Myofibrils, 481 Myoglobin, 115F hemoglobin compared with, 467–469, 468F, 468S oxygen binding in, 469 oxygen-binding cur ve for, 468F, 470 as oxygen-storage protein, 468 size of molecule, 90T structure of, 113, 468S Myohemerythrin, 141F Myoinositol, 189 Myosin, 481, 483, 483F–485F ATP hydrolysis and, 488–490 conformational change and, 497–498 definition of, 481D Myosin head, 484 Myosin V, 493F, 494–495 Myristic acid, 220T, 222G, 222 S Myristoyl, amide-linked, 257, 258F N-Myristoylation, 257, 258F Myristyl group, 1023 NAC, 989 NAD ϩ , in catabolism, 517, 522, 522F NAD ϩ -dependent dehydrogenase, 406, 579B NADH cytosolic, 620–623, 621F, 622F, 623T glycolysis and, 552–553, 553F as inhibitor of citrate synthase, 572 oxidation of, 599–601 in TCA cycle, 576 NADH-coenzyme Q reductase, 598 NADP ϩ anabolism and, 517 photosynthetic reduction, 633 NADPH, 2, 3S in anabolism, 523 ATP and, 840–841 in fatty acid synthesis, 722–723 glucose-6-phosphate and, 691–692, 691F hexose synthesis and, 647–648 NADPH-specific malate dehydrogenase, 657 NaK channel, 275–276 Na ϩ ,K ϩ -ATPase, 278 Naming of carbohydrates, 181 of chiral centers, 84B of chiral molecules, 80 of enzymes, 384–385 of genes, 1040B of polysaccharides, 194 of proteins, 1040B Nanotechnology, 302B Nascent chain-associated complex, 989 Natively unfolded protein, 168 Natriuretic peptides, 1021 ncRNA, 306 NDP, 296–297, 298F Near-attack conformations, 426–427, 445, 447 Negative control system, 917–918 Negative cooperativity, 458, 500–501 Negative entropy, 55 Negative regulation, 915 Negative supercoiling, 335F Negentropy, 52B Nelfinavir mesylate, 443S Nerve gas, 1052 Nervonic acid, 220T Neuraminic acid, 191 Neurodegenerative disorder, 988B Neurofibrillary tangle, 988B Neuroglia, 1043 Neurological disorders, 988B, 1054B–1055B Neuron, 1043, 1044F Neurotransmission pathway, 1044–1056 Neurotransmitter, 1046, 1047, 1052, 1056, 1056F Neutral pH, 36 Neutrality, 36 Neutrophil, 749 NFTs, 988B nhRNA, 940 Niacin, 524T Nicolson, G. L., 245 Nicotinamide adenine dinucleotide, 517, 522, 522F Nicotinamide adenine dinucleotide phos- phate, 517 Nicotinamide coenzymes, 568B Nicotinic acetylcholine receptor, 1047 Nicotinic receptor, 1047 Nitrate assimilation, 768, 769–770 Nitrate reductase, 769 Nitric oxide guanylyl cyclase and, 1024 hemoglobin and, 477B Nitrifying bacteria, 768 Nitrite reductase, 769 Nitrocellulose, 201B Nitro gen, 768–812 abundance of, 4 amino acid synthesis and, 779–810. See also Amino acid synthesis ammonium and, 774–776, 774F, 775F, 776F Escherichia coli glutamine synthetase and, 776–779, 778F excretion of, 810 inorganic, 768–774, 769F, 770F, 771F, 772F, 773F Nitrogen balance, 531 Nitrogen cycle, 769F Nitrogen fixation, 768, 771 regulation of, 773–774, 773F Nitrogenase, 771, 772 Nitrogenase reaction, 772–773, 772F Nitrogenase reductase, 771, 773G Nitrogenous base, 291–294, 292F, 293S, 294F p-Nitrophenylacetate, 431F, 438S N-linked glycoprotein, 205S, 207–208 N-linked saccharide, 204 NMDA receptor , 1052F NMR spectroscopy, 526–527, 527F NMT, 257 Nobel, Alfred, 201B Nomenclature. See Naming I-22 Index Noncoding RNA, 306 Noncompetitive inhibition, 400 Noncovalent bond, 11 Noncovalent interaction, in proteins, 134–136 Noncyclic photophosphorylation, 649 Nonessential amino acid, 781T Nonhistone chromosomal protein, 302–303, 336 Nonhomologous recombination, 877, 878 Nonidentical subunit, protein, 173 Nonlinear Lineweaver–Burk plot, 396B Nonoverlapping code, 953F Nonpolar amino acid, 74 Nonreceptor tyrosine kinase, 1023–1024 Nonreducing end, 192 Nonsense codon, 953 Nonsense mediated decay system, 946 Nonsense suppression, 960–961 Nonsteroidal anti-inflammatory drug, 750B–751B Nontemplate strand, 907B Norepinephrine, 1055B, 1056 Northern blotting, 364B Norvir, 443S NPY/AgRP-producing neuron, 854 NR I , 779 NR II , 779 N-terminal analysis, 102–103 N-terminal end, 100 NTP, 296–297, 298F Nuclear area of prokaryotic cell, 20T Nuclear envelope, 527 Nuclear magnetic resonance amino acids characterized by, 82–85, 84F spectroscopy, 526–527, 527F Nuclear pre-mRNA splicing, 941–942 Nuclease, 308–309 Nucleic acid. See also DNA; RNA base sequence of, 298S, 299 chemical synthesis of, 339–340 classes of, 299 definition of, 297D hybridization of, 332–333 hydrolysis of, 307–313 phosphodiesterases and, 308–309 restriction endonucleases and, 310–313, 311T, 312F restriction enzymes and, 310 specificity and, 309 primary structure of, 10S, 316–320, 317F, 318F, 321F secondary structure of, 320–333 denaturation and renaturation and, 330–333, 331F, 333F double helix and, 321–323, 322F, 323F, 326–327, 327F left-handed DNA and, 323–324, 325F, 326 right-handed DNA and, 323, 324F Watson–Crick base pairs and, 321 of virus, 21 Nucleoid, 20T Nucleoprotein, 120T Nucleoprotein filament, 880 Nucleoside, 294D, 295S Nucleoside diphosphate, 296–297, 297S in purine synthesis, 820–821 Nucleoside diphosphate kinase, 576, 666 Nucleoside monophosphate, 820–821 Nucleoside triphosphate, 296–297, 297S, 298F in purine synthesis, 820–821 Nucleosome, 302, 337F chromatin and, 336–337 chromatin-remodeling complexes and, 932 in eukaryotic gene activation, 934–935 Nucleotide, 291–315, 291D cyclic, 296, 296S nucleic acids and, 297–313. See also DNA; RNA nucleosides and, 295S phosphoramidite chemistry and, 340 purine, 813–821. See also Purine, synthe- sis of pyrimidines and purines, 291–294, 292F, 293S, 295F structure and chemistry of, 10S, 295–297, 296S, 297S, 298F sugar , 675, 675G, 675S thymine, 833–836, 834B, 835B, 836F Nucleotide binding, 832–833 Nucleotide excision, 887, 891 Nucleotide sequence completed genome, 367B DNA, 316–317 Nucleus of animal cell, 23T of eukaryotic cell, 20 function of, 8 of plant cell, 24T steroid hormones and, 763 Number, linking, 334 Nutrition, 531–532 amino acids required in, 781T carbohydrates and, 531, 680B fad diets and, 532B fasting state and, 673 fiber and, 532 lipids in, 531 protein requirement and, 531 vitamins and. See also Vitamin O antigen, 203–204 Obligate aerobe, 512 Obligate anaerobe, 512 Obligate coupling stoichiometry, 841–842 Obligatory substrate, 405 Octadecanoic acid, 219 Octyl glucoside, 245S 3-Octylthio-1,1,1-trifluopropan-2-one, 425B Odd-carbon fatty acid, 710–712 OEC, 638 Okazaki fragment, 864–865, 864F Oleander, 282B Oleic acid, 219, 220T, 221G, 221S Oleoyl alcohol, 230S Oligo(␣ 1,4→␣1,4)glucanotransferase, 674 Oligomer, 173 Oligomeric ion channel, 1047 Oligomycin, 618 Oligonucleotide degenerate, 362–363 gene chips and, 367–368 phosphoramidite chemistry and, 340 Oligonucleotide synthesis, solid phase, 341F Oligopeptide, 89D Oligosaccharide, 181D cleavage of, 208–209, 208S description of, 213 disaccharides as, 191–193, 192F N-linked, 207–208 O-linked saccharide, 204, 205S, 206F OMP decarboxylase, 828 Oncogene, 1029B Open promoter complex, 908 Open quaternary structure, 177 Open system, 48, 49F Operational code, 958 Operator, 913 Operon, 913 araBAD, 918–919 lac, 914F, 914–915 trp, 914, 920 Operon hypothesis, 914 Optical activity, 80 Optical properties of amino acid, 79–82 Optically active molecule, 82B ORC, 872 Order for reactant, 386 Ordered reaction, 403 Organ specialization, 847, 848F, 848T, 849–853, 851B, 851F Organelle, 1, 8F of animal cell, 23T function of, 7–8 of plant cell, 24T in prokar yotic cell, 20 Organic molecule in photosynthesis, 650–656, 651F, 651G, 653T, 654F, 655F Ori sequence, 355 Origin of replication, 355, 862–863 Origin recognition complex, 872 Ornithine, 783, 784F Ornithine transcarbamoylase, 783 Orotate phosphoribosyltransferase, 828 Orthogonal synthesis, 119 Osmosis, 45 Osmotic pressure, 34, 34F Osteoblast, 282 O-succinylhomoserine, 790 Outer membrane, 592 porins in, 255 Ovalbumin gene, 939 Overall activity site, 831 Overlapping code, 953F Oxaloacetate, 780S NAD ϩ -dependent dehydrogenase and, 579B Oxidase, mixed-function, 762 Oxidation alpha of fatty acids, 714, 716 in Refsum’s disease, 717B beta, 701F, 701–702, 704–709, 704F of D-glucose, 188S of fatty acids, 701–702, 701F, 704F, 713–714, 714F, 717 glucose, 622–623, 623T migratory birds and, 709–710 of NADH, 599–601 of palmitoyl-CoA, 709T Index I-23 prostaglandins and, 747 in Refsum’s disease, 717B of succinate, 601–603, 602F Oxidation reduction, 636 Oxidative cleavage of disulfide bridges, 102F Oxidative phosphorylation, 522, 563, 592–629 cytosolic NADH and, 620–623, 621F, 622F, 623T inhibitor of, 616–618 isocitrate dehydrogenase and, 574 as membrane-associated process, 592–593 mitochondrial, 620 organization of, 597–611, 597F, 598F, 600B, 604G, 606F, 610F proton gradient and, 611–620, 614F, 616F–618F, 619B, 619F reduction potentials and, 593–596, 594F, 595T thermodynamics and, 611 2,3-Oxidosqualene lanosterol cyclase, 757 Oxygen abundance of, 4 aerobic organisms and, 512 cytochrome c and, 606–607 hemoglobin and, 472B in metabolism, 511 in myoglobin, 469 in water, 28–29 Oxygen binding by hemoglobin, 469 Oxygen cycle, 512 Oxygen dissociation, 473–475 Oxygen evolution, 640, 640F 18 Oxygen exchange, 613–614 Oxygen saturation curve, 474F Oxygenation, hemoglobin and, 469, 471 Oxygen-binding curve of hemoglobin, 468F, 470–471 of myoglobin, 468F, 470 Oxygen-binding heme protein, 113 Oxygen-evolving complex, 638, 645, 645F Oxygen-storage protein, 468 Oxyhemoglobin, 473 Oxytocin, 482B P680, 637 P700, 637, 645 P870, 642 P protein, 444 p21 protein, 260 P site, 965 PA700, 1000 PAF, 226, 227B Pair diastereomeric, 184 Watson–Crick base, 301S, 321 Pairing chromosome, 878 codon–anticodon, 958–961, 959F, 959T, 961T intrastrand base, 342, 344–345, 346, 348 Palindrome, 327, 916 Palmitate synthesis, 728F Palmitic acid, 219 beta-oxidation of, 708–709 structure of, 220T, 221G, 221S Palmitoleic acid, 220T, 222G, 222S Palmitoyl-CoA in fatty acid synthesis, 726–727 oxidation of, 709T sphingolipid synthesis and, 744–745 Pancreatic juice, 699F Pancreatic ribonuclease A, bovine, 94F Pantothenic acid, 524T, 570B Papillomavirus E1 protein, 501F PAPS, 796 Parallel beta-pleated sheet, 143 Parallel chain in chitin, 198 Parallel sheet in proteins, 143 Paralogous proteins, 113 Parkinson’s disease, 600B, 988B Particle ribonucleoprotein, 941 signal recognition, 995 small nuclear ribonucleoprotein, 305 Partition properties of amino acid mix- tures, 85 Parvalbumin, 1031 Passenger strand, 375 Passive diffusion, 271, 272F Pasteur, Louis, 82B “Pasteur effect,” 560 Patch recombinant, 880 Pathway. See also Cycle for ammonium biosynthesis, 769F anabolic, 520–521 cyclic electron transfer, 641 of cyclic photophosphorylation, 650F of dTMP synthesis, 834F electron-transport, 563 Embden-Meyerhof, 535, 536F gluconeogenesis, 663–665, 664F glycolytic, 520 Hatch–Slack, 656–659 inorganic nitrogen and, 768–774, 769F–773F Leloir, 556–557 for light-regulated reduction of Calvin cycle enzymes, 655F metabolic, 527, 528F, 529F methyl-directed, 889B neurotransmission, 1044–1056 of ornithine biosynthesis, 784F of palmitate synthesis, 728F pentose phosphate, 684–693. See also Pentose phosphate pathway polyol, 687B for purine catabolism, 823, 824F saccharopine, 809 shikimate, 798, 799F signal transduction, 257, 992–993, 1010–1013, 1012F transduction, 1031F Pauling, Linus, 139, 143B, 419 PCNA homotrimer , 874F, 874G PCNA protein, 874 PCP, 1052 PCR, 373–375, 374F, 375F PCR-based muta genesis, 375F PDZ domain, 1004 Pelouze, Theophile, 201B Penicillin, 402F, 403 Pentose, 294 Pentose phosphate pathway, 684–693, 685F gluconolactonase and, 684 glucose-6-phosphate dehydrogenase and, 684, 685F in liver and adipose cells, 684 nonoxidative steps in, 686–690 oxidative steps in, 684–686, 685F 6-phosphogluconate dehydrogenase and, 684, 686 phosphopentose epimerase in, 687–688 phosphopentose isomerase in, 686–687, 687F transaldolase in, 689–690 transketolase in, 688–689, 688F Pentraxins, 213T, 215 Pentulose, 183 PEP chorismate synthesis and, 798 formation of, 63, 63F in glycolysis, 549–550, 549F, 551F hydrolysis of, 57 PEP carboxykinase, 664, 666–667, 666F PEP carboxylase, 582, 583F Pepsin, 384, 437 Peptidase, 994, 996–997 Peptide agouti-related, 854 chemistry of, 89 classification of, 89 leader, 994 polypeptide chains of, 89 signal, 996–997 solid-phase synthesis of, 118F vasoactive intestinal, 1056 Peptide acid hormone, 1008D Peptide bond, 71D handedness of, 138B of protein, 86–87, 87F, 88F, 136 Peptide chain elongation of, in eukaryotes, 981 initiation of, 966–968, 966F, 967F, 969T in eukaryotes, 976–979, 977F in maltoporin, 255F termination of, 974, 975F in eukaryotes, 981 in protein synthesis, 974, 975F Peptide mass fingerprinting, 108–109 Peptide neurotransmitter, 1047 Peptidoglycan, 201, 202S Peptidyl site, 965 Peptidyl transfer, 969 Peptidyl transferase, 964, 969, 971f Peptidyl transferase center, 969 Peptidyl transferase reaction, 411–412, 412F Peridinin-chlorophyll protein, 169F Peripheral protein, 246 Periplasmic space, 203 Perkin condensation, 571 Permanent dipoles, 13 Peroxisomal beta-oxidation of fatty acids, 714 Peroxisome, 20, 23T, 24T Peroxisome proliferator -activated receptor ␦, 708B Pest control, 257B PET, 555B PFK-2, 671 pH, 35–40, 36T alpha-helix and, 142 of amino acids, 71, 74 I-24 Index pH (continued) buffers and, 41–44, 41F of common fluids, 36T denaturation of DNA and, 331 enzymatic activity and, 396–397, 397F gastric H ϩ ,K ϩ -ATPase and, 280 of glycine, 76 hydrolysis of ATP and, 64, 64F respiration and, 44B standard-state free energies and, 54–55 Phage T4 DNA ligase, 357 Pharmaceuticals, enzymes and, 386 Phase transition, 263–264, 264T Phencyclidine, 1052 Phenyl fatty acid, 701F, 704F Phenylalanine catabolism of, 809–810, 809F pK a value for, 77T structure of, 73S synthesis of, 798–799, 800F tRNA, 346F–347F, 347G ultraviolet light absorbed by, 82 Phenylalanine-4-monooxygenase, 799 Phenylketonuria, 810B Phenylthiohydantoin amino acids, 86, 86F Pheophytin, 640 Phorbol ester, 1036F Phosphatase, naming of, 384 Phosphate, enol, 63 Phosphate compound, high-energy, 56, 57T Phosphate ester of monosaccharides, 189 Phosphate system, 41–42 Phosphate-linked base, 342S Phosphatidic acid, 223G, 223S, 224 Phosphatidylcholine, 225G, 1031 Phosphatidylethanolamine, 225, 738, 741, 741F Phosphatidylglycerol, 225G Phosphatidylinositol, 225G, 737, 1029 Phosphatidylinositol-4,5-bisphosphate, 1029 Phosphatidylserine, 741, 741F Phosphinothricin, 801B Phosphite-linked base, 342S 3Ј-Phosphoadenosine-5Ј-phosphosulfate, 796 Phosphodiester, cyclic, 296, 296S Phosphodiester bridge, 297, 298S Phosphodiesterase, 308–309 Phosphoenolpyruvate, 549, 583F chorismate synthesis and, 798 formation of, 63, 63F free energies of hydrolysis of, 57T in glycolysis, 549–550, 549F, 551F Phosphoenolpyruvate family of amino acids, 781T Phosphoethanolamine transferase, 741 Phosphofructokinase, 542–543, 542F, 542G, 543B, 543F–544F Phosphofructokinase-2, 671 Phosphog lucoisomerase, 541, 541F, 543B Phosphoglucomutase, 556 Phosphoglucomutase reaction, 447B 6-Phosphogluconate dehydrogenase, 684, 686, 686F Phosphoglycerase kinase, 547–548, 547F 3-Phosphoglycerate, 650, 793 3-Phosphoglycerate dehydrogenase, 793 Phosphoglycerate family of amino acids, 793–796, 796F Phosphoglycerate kinase, 167F Phosphoglycerate mutase, 431T in glycolysis, 547F, 548, 549F Phosphoglycolohydroxamate, 426 F Phosphohistidine, 576 3-Phosphohydroxypyruvate, 793 Phospholipase, 234B, 234F, 235, 1028 Phospholipase A 1 , 234F Phospholipase A 2 , 234F Phospholipase C, 1029–1031 Phospholipid, 223–227, 234B, 234F eukaryotes synthesizing, 741–743 glycerophospholipid, 223–227, 223G, 223S, 224S, 225F, 225S, 226F, 227B Phosphomannoisomerase, 556 Phosphopantetheine group, 727 Phosphoprotein phosphatase-1, 466, 679 Phosphoramidite, 340 Phosphoramidite derivative of nucleotides, 342S Phosphorelay system, 1034B Phosphoribosyl transferase, 821 Phosphoribosyl-anthranilate, 801 Phosphoribosyl-anthranilate transferase reaction, 799 Phosphoribulose kinase, 653 Phosphoribulosylformimino-5-aminoimida- zole-4-carboxamide ribonu- cleotide, 804 Phosphoric acid hydrolysis of anhydrides of, 59–60 titration curve for, 40, 41F Phosphoric-carboxylic anhydride, 61, 63 Phosphorolysis, 462 Phosphoryl group transfer reaction, 58F Phosphorylase backbone structures of, 167F glycogen, 462S, 462–467, 463F, 463S, 464F, 674, 675F Phosphorylase a, 466 Phosphorylase b, 466 Phosphorylase cascade, 681–683 Phosphorylase reaction, starch, 196S Phosphorylation of acetyl-CoA carboxylase, 723F, 726–727 description of, 461–462 of glucose, 539 in histone code, 934 oxidative. See Oxidative phosphorylation of phosphofructokinase, 542–543, 542F, 542G, 543B, 543F–544F in TCA cycle, 575–576 Phosphorylation potential, 844 Phosphorylation–dephosphorylation cycle, 736, 1036 3-Phosphoserine, 793 Phosphotriesterase, 159F Photoautotroph, 512T Photochemical apparatus, 841 Photoheterotroph, 512T Photolyase, 890 Photophosphorylation, 643, 643F, 648, 649–650, 649 F Photoreactivating enzyme, 890 Photorespiration, 656–659, 656D Photosynthesis, 630–661 carbon dioxide in, 650–659 limited fixation of, 656–659, 657F, 658F organic molecules from, 650–656, 651F, 651G, 653T, 654F, 655F chlorophyll-captured solar energy in, 633–634, 634F, 634S, 635F, 635S, 636–637, 636F general properties of, 630–633 light-driven A TP synthesis in, 649F, 650F photosynthetic reaction centers in, 641–647, 642F, 643F, 643G, 646F photosystems in, 637–641, 638F, 640F quantum yield of, 647–648 Photosynthetic pigment, 634, 636 Photosynthetic reaction center, 641–647, 642F, 643F, 643G, 646F Photosynthetic unit, 637, 637F Photosystem, 637–641, 638F, 640F Phototroph, 511D, 841 Phototrophic organism, 56 pH-rate profile, 440F Phylloquinone, 645 Phytanic acid-␣-hydroxylase, 716 Phytanic acid-␣-oxidase, 716 Phytol, 230S, 633 PI, 1029, 1031B PI-88, 207B Pi gment, 634, 635S, 636 ␣-Pinene, 230S Ping-pong reaction, 404, 406–407 in fatty acid synthesis, 724 PIP, 1029 Pit, coated, 758 Pitch, 321 Pizzarello, Sandra, 83B pK a , 38, 40, 42, 42F, 77T Plane, amide, 87 Plant desert, 659 isoprene emitted from, 231B photosynthesis in, 630–661. See also Photosynthesis Plaque amyloid, 988B atherosclerotic, 155B dental, 196 Plasma, 43B Plasma membrane, 19, 23T, 24T, 242, 243, 243F Plasmalogen, 227, 743–744, 743F Plasmid, 333 chimeric, 355 in cloning, 354–360, 354D, 355F, 356F, 358F, 359F recombinant, 357 as shuttle vector, 360 Plasmid vector, 356F Plastid, 19, 631 Plastocyanin, 641 Plastocyanin:ferredoxin oxidoreductase, 641 Plastoquinone, 640, 640S Platelet-activating factor, 226, 227B, 1038F in lipid synthesis, 744, 744F Pleated sheet, -, 142–144, 143B, 144F Plot Hanes–Woolf, 395, 396F Lineweaver–Burk double reciprocal, 395 Ramachandran, 137, 138F Van’t Hoff, 50 Plus end of microtubule, 490 P/O ratio, 620 Point, isoelectric, 97 Point mutation, 891–892, 892F . complex, 990–992, 992F, 992G Groove, major or minor, 322 Group, prosthetic, 598 Group transfer potential, 58–59, 59T Growth, 839–840 Growth factor, 212, 829B Growth factor receptor , 1016 Growth. lipoprotein, 757 High-energy biomolecule, 57–63 High-energy bond, 58 High-energy bond transfer potential, 59T High-energy phosphate compound, 57, 57T High-performance liquid chromatography, 86,. 760–761 Hyperchromic shift, 330 Hyperpolarization, 1053 Hyperuricemia, 825 Hyperventilation, 44B Hypothesis lock-and-key, 409–410 Mitchell’s chemiosmotic, 609 operon, 914 wobble, of codon–anticodon