See also Muscle contraction.
Trang 1substrates 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, 203F
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 5-diphosphate, 296 Guanosine 5-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/2eratio, 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 Helling, 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, 477B
oxy and deoxy forms of, 473
oxygen binding of, 468F, 469–471
pathological sequence variants of,
117T proteins of, 113, 115F
quaternary 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
Trang 2Hexokinase, 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
pKavalue 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,K-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, 433B 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
Trang 3Immunodeficiency 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
butterfly, 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
IP3, 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
pKavalue 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
Trang 4Isopropylmalate 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
Ka, 36–37
Kappa gene family, 899
kcat, 393, 393T
kcat/Kmratio, 393–394
KcsA, 274
Keq, 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, regulation 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
Kw, 35 Label, affinity, 402
lac operon, 914F, 914–915 lac repressor, 915, 915F, 917B, 917T
-Lactalbumin, 116, 116G
-Lactamase, kcat/Kmratio 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
pKavalue 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-harvesting 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
Trang 5sphingolipids, 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, 853F
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
Lyase
ATP-citrate, 724
HMG-CoA, 718
Lycopene, 230S
Lymphocyte homing receptor, 212 Lysine
catabolism of, 809
pKavalue 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, 279G, 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
Trang 6Metabolic 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, 528F, 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
pKavalue for, 77T
structure of, 73S, 75
synthesis of, 790, 791F
Methionyl-tRNAifMetformyltransferase,
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
Mg2channel, 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 F1F0–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, 176F 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, 663B 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
Trang 7Motor 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
3-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 curve 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, 222S Myristoyl, amide-linked, 257, 258F
N-Myristoylation, 257, 258F
Myristyl group, 1023 NAC, 989
NAD, in catabolism, 517, 522, 522F
NAD-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
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,K-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
Nitrogen, 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
Trang 8Noncoding 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
NRI, 779
NRII, 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 prokaryotic 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-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
ofD-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
Trang 9prostaglandins 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
18Oxygen 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 mutagenesis, 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
Trang 10pH (continued)
buffers and, 41–44, 41F
of common fluids, 36T
denaturation of DNA and, 331
enzymatic activity and, 396–397, 397F
gastric H,K-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
pKavalue 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
3-Phosphoadenosine-5-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
Phosphoglucoisomerase, 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, 426F
Phosphohistidine, 576 3-Phosphohydroxypyruvate, 793
Phospholipase, 234B, 234F, 235, 1028
Phospholipase A1, 234F
Phospholipase A2, 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, 649F
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 ATP 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 Pigment, 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
pKa, 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