Biochemistry, 4th Edition P118 doc

Index I-25
Polar bear, 223B
Polar solute, 31
Polarity
of protein polypeptide, 89
structural, 10
of water, 30
Poly(A) polymerase, 941
Poly(A) tail, 303, 940
3Ј-Polyadenylation of eukaryotic mRNA,
940–941
Polyadenylylation, 940
Polyalanine, 142
Polyamino acid, 142
Polycistronic mRNA, single, 912–913
Poly(Gly-Pro-Pro), 151F
Polyleucine, 142
Polylinker, 357
Polymerase
core, 907
DNA, 317, 863–864, 865–870, 865T,
866F, 867T, 868F, 868G, 869T,
870B, 870F, 874
poly(A), 941
RNA
in eukaryote, 924–925, 925G, 926T
in prokaryote, 908, 909F, 910–911
Polymerase chain reaction, 373–375, 374F,
375F, 377F, 378F
Polymerization
initiation of, 911

microtubule, 494B
by open quaternary structures, 177
Polyneuropathy, familial amyloidotic, 172B
Polynucleotide, 297
Polynucleotide chain, cleavage in, 309F
Polynucleotide fragment, 316–317
Polyol pathway, 687B
Polypeptide, 89D
backbone, 167D
folding of, 96F, 96G, 146
Hsp70 chaperones and, 989
laboratory synthesis of, 117, 119
polarity of, 89
in pyrimidine synthesis, 828
structure of, 10S
synthesis of, 118F, 119
Polypeptide chain, 89
conformation of, 96–97
in E. coli polymerase, 866
fragmentation of, 103–105, 104F, 105T
separation of, 101
twist in, 166F
Polypeptide hormone, 1010
Polyprenol, 231
Polyprotic acid, weak, 76–78
Polyribosome, 976
Polysaccharide, 181D, 194D
in bacterial cell walls, 201–204, 202S,
203F
branched, glycogen and, 674

cell surface, 204
description of, 213
function of, 194–195
naming of, 194
storage, 194
structural, 196–201
structure of, 10S
Polysome
electron micrograph of, 976F
in protein synthesis, 976, 976F
Polyunsaturated fatty acid, 219D
degradation of, 714, 715F
docosahexaenoic acid as, 736B
in mammals, 735
Porcine ribonuclease inhibitor, 169
F
Porin, 255, 258F, 593
Portal vein system, 680, 680F
Positive control system, 917–918
Positive supercoiling, 335F
Positron emission tomography
, 555B
Postsynaptic cell, 1046
Post-transcriptional processing of mRNA,
940–941
Post-transcriptional regulation of gene
expression, 979
Post-translation modification of protein,
119, 993
Potassium

action potential and, 1044–1046,
1045F
transport of, 272–274
Potassium channels, 272, 274, 274F–275F
Potassium ion, hydrolysis of ATP and, 64
Potential
action, 1044–1046, 1045F
electrical, in neuron, 1044
electrochemical, 271
group transfer, 58–59
phosphorylation, 844
reduction, 593–596, 594F, 595T
thermodynamic, 66
transfer, types of, 59T
Potentiality, thermodynamic, 382
Power, catalytic, 383
Power stroke, 489
PPT, 801B
pp60
v-src
, 1023
Precursor
inosinic acid as, to GMP and AMP, 814,
815F, 816–818, 820F
to plasmalogens, 743–744
zymogens as, 454–455, 454F–455F,
454T
Pregnenolone, 238S, 763
Prehybridization, 364B
Preinitiation complex, 931–932, 977F, 978

Prenyl, thioether-linked, 257
Prenylation reaction, 259B
Prephenate, 799
Preproalbumin, 995
Preprohormone, 1010
Prepro-opiomelanocortin, 1010
Prereplication complex, 872
Pressure, osmotic, 34, 34F
Presynaptic cell, 1046
Pribnow box, 908
Primary structure
fundamental, 86–89, 87F, 88F, 89, 90T
of nucleic acids, 316–320, 317F, 318F,
321F
of protein, 94F, 100–110. See also Amino
acid sequencing
Primase, 869
Primed synthesis method, 317
Primer, 317, 865
Priming reaction in glycolysis, 538, 541F,
542–543, 542F
Prion, 893, 895
Prion protein, 893, 895
Pro ␣-2 collagen gene, 940
Probe
heterologous, 363
in Southern blotting, 364B
Processive movement, 500
Prochirality, 224S
Product formation, 391

Proenzyme, 434, 454, 454F
Progesterone, 233, 234S, 763
Proinsulin, 454, 454F
Projection
Fischer, 183–185
Haworth, 185–187
Prokaryote
gene transcription in, 906–912, 909F,
910F, 911F, 913F
reg
ulation of, 912–923, 914F, 915F,
916T, 917B, 917T, 918F, 918G,
919F, 921F, 922F
metabolic diversity of, 511
metabolic pathways in, 527
mRNA in, 304F
peptide chain initiation in, 966–968,
967F
ribosomes of, 305F,
962–963
RNA polymerases, 906–907
translocation of proteins in, 994
Prokar
yotic cell, 17, 20, 20T
Prokaryotic promoter, 908, 910–911
Prolactin, 1009F
Proliferating cell nuclear antigen, 874
Proline
hydroxylated residues of, 150S
pK

a
value for, 77T
structure of, 72S, 150S
synthesis of, 783
Proline racemase, 423
Proline racemase reaction, 423F
Prolyl hydroxylases, 559
Promoter, 357, 907
cloning, 357
in eukaryote, 927, 928F
prokaryotic, 908, 910–911
Promoter complex, 908
Propeller twist, 323, 323F
Propionyl-CoA, conversion of, 711F
Prostaglandin, 737, 747, 747B
Prostaglandin endoperoxide H synthase,
747, 749F
Prosthetic group, 81B, 120, 385, 598
Protease
aspartic, 437, 440–441, 441F, 441S
HIV-1, 440F, 441–442
HtrA, 1003
naming of, 384
serine, 434–437, 436F, 438F, 439B
Proteasome, 947, 998, 1000
Proteasome activator-700 kD, 1000
Proteasome inhibitors, 425B, 1003B
Protein. See also Protein synthesis
acetylcholine transport, 1050
actin-anchoring, 486B

amino acid sequences of
analysis of, 99–100
databases of, 109–110
nature of, 110–117, 110F, 113F, 114F,
115F, 116G, 117T
in structure, 136
annexin, 1031
biological functions of, 120–123
biotin carboxyl carrier, 724
I-26 Index
Protein (continued)
calcium-binding, 1031
cAMP receptor, 917
catabolite activator, 916
catalytic, 121
chemistry of, 93
cholesterol ester transfer, 758
classification schemes for, 157–159
of cloned genes, 369–372, 369F, 371F
coiled-coil motif in, 148B
conjugated, 120T
definition of, 89D
degradation of, 208–209, 998–1005,
999F, 1000F, 1001F, 1004B, 1004F
denaturation of, 51T, 159–161, 160F
DNA-binding, 923
domains of, 155–156
EF hand, 1031, 1033
energy in, 698T
in eukaryotes, 995

extrinsic, 246
in fatty acid synthesis, 727, 727F
folding of, 987–992
diseases of, 172B
of globular protein, 166–167
Hsp70 chaperones for, 988–989, 989F
hydrophobic interactions in, 135
mechanism of, 162–163, 163F
molecular chaperones for, 168
N-linked oligosaccharides in, 209B
polypeptide, 96F, 96G, 146
thermodynamics, 163–164
functions of, 120–123
fusion, 371T
G
GPCR signals transduced by,
1024–1025
muscarinic receptors and, 1050–1052
phospholipase C activation by, 1030
as signal transducer, 1027–1028
gene regulatory, 935–939, 939F
globular, 152–170. See also Globular
protein
green fluorescent, 81B, 81G, 372
GTP-binding, 466
heat shock, 168, 988
with helix-turn-helix motif, 936
hybrid, 371F
hydrophobic, 203
indirect readout and, 937

inte
gral, 246
integral membrane, 270
intrinsic, 246
intrinsically unstructured, 168, 170F
iron–sulfur, 598
isolation and purification of, 97–98,
98B, 99T
link, 213
lipid-anchored, 256–258, 257B, 258F, 260
location in cell, 994F, 994–998, 996F,
997F
membrane, 248–260, 995
aggregation of, 272–273
bacteriorhodopsin as, 250–251, 251F
porins as, 255, 258F
with single transmembrane segment,
249–250, 249F
as switching device, 256–258, 257B,
258F, 260
mitochondrial, 997
motor, 481
multifunctional, 725
multimeric, 175F
mutant, 117, 171
B
noncovalent interactions in, 134–136
nonhistone chromosomal, 302–303, 336
nutritional requirement for
, 531

oligomeric state of, 458–459
oxygen-storage, myoglobin as, 468
peripheral, 246
post-translation modification of, 993
primary structure of
architectural arrangement of, 93–97,
94F, 95F, 96G, 97F
fundamental, 86–89, 87F, 88F, 90T, 93
prion, 893, 895
quaternary structure of, 173–178
polymerization of, 178
symmetry of, 174, 176F
variety of, 177
weak forces in, 174, 176
ras, 259B, 1027, 1027G
RecA, 881–883
receptor, 1043
regulatory, 913
ribosomal, 962
Rieske, 604
Ruv, 880, 883–885
scaffolding, 266–267
secondary structure of, 136–146
alpha-helix in, 137, 139–142, 140F,
141F
amide plane in, 136–137, 137F, 138F
beta-pleated sheets in, 141F, 142–144,
143B, 144F
beta-turns in, 144–145, 145F
parallel sheets in, 143

simple, 119
single-stranded DNA-binding, 863
size of molecules of, 90T
SMC, 338–339, 339F
structure of, 169F
targeting of molecules by, 121–122
tertiary structure of, 146–172
fibrous proteins and, 146–151, 147F,
149F, 150S, 151F, 151S
globular proteins and, 152–170. See
also Globular protein
marginal stability of, 164
triage of, 1004B
Tus, 870
ubiquitin-carrier, 998
unfolding of, 55, 55F
viral transforming, 1023
whimsical names for, 1040B
Protein binding, 122
Protein deposit, diseases with, 988B
Protein interaction domains, 1011
Protein isoform, 944
Protein kinase
covalent modification and, 453
description of, 453F, 460–461
mitogen-activated, 1034B
Protein kinase A, 460, 460F, 1035
Protein kinase C, 1029–1031, 1035–1036
Protein phosphatase 2A, 693
Protein sequence, conventions used in

expressing, 907B
Protein splicing, 896B
Protein synthesis, 952–986
aminoacyl-tRNA synthetases in, 953,
955–958, 955T, 956F, 957G
codon–anticodon pairing in, 958–961,
959
F, 959
T, 961T
Escherichia coli glutaminyl-tRNA syn-
thetase in, 958, 958G
in eukar
yotic cells, 976–984, 977F, 978T,
980B, 980F, 982T
genetic code and, 952–953, 953F, 954B,
954T
G:U base pair in, 958
inhibitors of, 981–984, 982T
messenger RNA and, 303
mRNA translation in, 965–976. See also
mRNA translation in protein syn-
thesis
ribosomes in, 961–965, 962T, 963F,
965T
steps in, 965F
Protein transfer potential, 59T
Protein translocation, 994
Protein tyrosine kinase pp60
c-src
, 1036,

1036F
Protein tyrosine phosphatase SHP-2,
1036–1037, 1036G
Protein-coding gene, 925–926
Protein-protein interaction, 123, 372–373,
922–923
Proteoglycan, 209–213
cell growth and, 211–212
function of, 209–211
Proteoglycan-hyaluronate aggregate, 213
Proteolytic cleavage in post-translational
processing, 993
Proteolytic enzyme
digestive, 454–455, 454F
in polypeptide cleavage procedures,
105T
Proteome, 120
Proteomics, 367B, 513
Prothrombin, 232B
Proton gradient
flagella and, 503–504
synthesis of ATP and, 611–620, 614F,
616F–617F, 618F, 619B, 619F
Proton pump, 283F
Proton symport, 286
Proton transport, 604–605
Proto-oncogene, 1029B
Provirus, 877
Prozac, 1054B–1055B
PrP, 893, 895

PRPP in Lesch-Nyhan syndrome, 822B
PS decarboxylase, 741
PsaD, 645
Pseudoknot formation, 344
Pseudosubstrate sequence, 460, 845
Pseudouridine, 305S, 345
PSI complex, 637–638, 638F, 640, 645,
646F, 647
PSII complex, 637–638, 638F, 640–641
D-Psicose, 183S
Pump, proton, 283F
Pure noncompetitive inhibition, 400
Purification
affinity, 97
protein, 98, 99T
Index I-27
Purine, 291–294, 292F, 293S
catabolism of, 821, 823–826, 824F, 826F
salvage of, 821, 821F
synthesis of, 802, 804, 813–821
ATP-dependent kinases in, 820–821
inosinic acid in, 814, 815F, 816–818,
819F
regulation of, 819–820
Purine nucleoside cycle, 823, 824F
Purine nucleoside phosphorylase, 823
Purine ring, 292F
Puromycin, 983S
Purple patches, 285
Pyranose, 184

Pyranose form
of
D-glucose, 186S
of
D-ribose, 186S
Pyridoxine, 524T
Pyrimidine, 291–294, 292F, 293S
degradation of, 830, 830F
fluoro-substituted, 835B
synthesis of, 826–830, 827F, 828F
Pyrimidine dimer repair, 890
Pyrimidine ring, 292F
Pyroglutamic acid, 75S, 76
Pyrophosphate, 57T
Pyrophosphomevalonate decarboxylase,
755
Pyrrolysine, 75S
Pyruvate
gluconeogenesis and, 662
in glycolysis, 552–553, 553F
glycolysis production of, 537F
metabolism of, 552–553, 553F
synthesis of, 805F
transamination of, 851F
in tricarboxylic acid cycle, 564F, 566
Pyruvate carboxylase, 582, 664–665
compartmentalized, 666
in gluconeogenesis, 665–666, 665F
Pyruvate decarboxylase, 553
Pyruvate dehydrogenase complex, 566,

567F, 568B–569B, 571F
Pyruvate dehydrogenase E3-binding pro-
tein, 566
Pyruvate dehydrogenase kinase, 584–586
Pyruvate dehydrogenase reaction, 566
Pyruvate family of amino acids, 781T, 793,
794F, 795F
Pyruvate kinase, 550–551, 550F, 552F
Pyruvate-Pi dikinase, 658
Pyruvic acid, 191S
PYY
3–36
, 855
Q cycle, 603, 604–606, 605F
Q
a
-SNARE, 268
Q
bc
-SNARE, 268
Quadruplexes, 329, 330F
Quality control, protein, 1003–1005,
1004B
Quantum yield of photosynthesis, 637,
647–648
Quaternary structure
allosteric properties and, 467–468
of hemoglobin, 469, 471
of protein, 95, 173–178
Racker, Efraim, 616

Radiation, ultraviolet, 82
Radical, free
cationic, 636, 638
in ribonucleotide reduction, 832F
RAG recombinase, 901
Ramachandran plot, 137, 138F
Random coil, 153
Random reaction, 403
RANTES, 1042
Ras protein, 259B, 1027, 1027G
Rat cartilage proteoglycan, 210F
Rat growth hormone gene, 889B
Rate constant, 386
Rate of enzyme catalysis, 386, 419
Rate-limiting step, 437
Ratio, 393
equilibrium, ATP changing, 67B
H
ϩ
/2e
Ϫ
, 611
k
cat
/K
m
, 393–394
molar, of nucleic acids, 300T
P/O, 620
Rational drug design, 404B

Reactant, 386
Reaction
aminotransferase, 782B
anaplerotic, 582, 584
beta-oxidation, 704–709, 704F, 706F
bimolecular, 387
in Calvin–Benson cycle, 653, 653T, 655
DNA strand exchange, 881–883
filling up, 582, 584
fructose-1,6-bisphosphatase, 667
in gluconeogenesis, 665–669, 667F,
668F, 669F
glucose-6-phosphate dehydrogenase,
684, 685F
glutamine synthase, 776F
glycogen phosphorylase, 462–467, 462S,
463F, 463S, 464F, 674, 675F
glycogen synthase, 676, 678F
of glycolysis, 538T
malate dehydrogenase, 578
nitrogenase, 772–773, 772F
nucleoside diphosphate kinase, 576
PEP carboxykinase, 666F
6-phosphogluconate dehydrogenase,
684, 686, 686F
phosphopentose isomerase in, 686–687,
687F
photosynthetic, 632–633, 632F
priming, 538
redox, 595–596

ribulose-1,5-bisphosphate carboxylase,
651, 651F
second-order, 387
serine dehydratase, 807B
splicing
, 942–943
succinate dehydrogenase, 576
thymidylate synthase, 836F
transaldolase, 689–690, 690F
transamination, 782B
transketolase, 688–689, 688F
in tricarboxylic acid cycle, 572T
UDP-glucose pyrophosphorylase, 676,
676F
Reaction center, photosynthetic, 638,
641–647, 642F, 643F, 643G
Reaction half-cell, 594
Reactive-center loop, 171B
Readout, indirect, 937
Reagent, Edman’s, 102
Reannealing, 331
RecA, 499
RecA protein, 881–883, 882G
RecBCD enzyme, 880
RecBCD-dependent initiation of recombi-
nation, 881F
Receptor
acetylcholine, 1047, 1048F
asialoglycoprotein, 209
G-protein-coupled, 1013, 1015

lambda, 255
LDL, 760
lymphocyte homing, 212
muscarinic, 1050–1052
nicotinic acetylcholine, 1050
nitric oxide, 1024
signal-transducing, 1012F, 1013–1024,
1013F, 1013G, 1024B
TMS, 1015
Receptor protein, 1043
cAMP
, 917
Receptor signal transduction, 1024–1034
Receptor tyrosine kinase, 1016–1017, 1030,
1030F
Recognition matrix, 937
Recognition particle, signal, 995
Recombinant DNA, 354–381
artificial chromosomes from, 360
cloning and, 354–360. See also Cloning
directed changes in heredity and,
375–377, 377F, 378B, 378F
DNA libraries and, 360–368, 361B,
362
F–363F, 364B, 365F, 366F,
367B, 368F–370F, 371T
polymerase chain reaction and,
373–375, 374F, 375F
Recombinant DNA molecule, 354
Recombinant plasmid, 355

Recombinase, 881
Recombination, genetic, 877–886. See also
Genetic recombination
Recombination-activating gene, 901
Recombination-dependent replication,
884B, 885
Recycling factor, ribosome, 974
Red blood cell, sickle cell anemia and,
476–478
Red wine, polysaccharide in, 199B
Redox couple, 594
Redox reaction, 595–596
Reducing end, 192
Reducing sugars, 188
Reductase
aldose, 687B
nitrogenase, 771, 773G
Reduction
of ␤-carbonyl group, in fatty acid synthe-
sis, 729–730
oxidation, transduction of light energy
and, 636
Reduction potential, 593–596, 594F, 595T
concentration and, 596
Reductive citric acid cycle, 583B
Reductive cleavage, of disulfide bridges,
102F
Reentrant loops, 253
Reference half-cell, 594
Refsum’s disease, 717B

I-28 Index
Regular structure, of protein, 94F
Regulation
allosteric. See Allosteric regulation
autogenous, 920
of carbon dioxide fixation, 655–656,
655F
by enzyme, 383–385
of gene transcription, 912–923, 914F,
915F, 916T, 917B, 917T, 918F,
918G, 919F, 921F, 922F
of gluconeogenesis, 669–673, 671F, 672F
of glutamine synthetase, 776–779, 777F,
777G, 778F
of glycogen metabolism, 678–683
of glycogen synthase, 676–679
of isocitrate dehydrogenase, 586
metabolic, 16
negative, 915
of nitrogen fixation, 773F
of phosphofructokinase, 542G
post-transcriptional, 979
of purine synthesis, 819–820, 820F
of pyrimidine synthesis, 830
of tricarboxylic acid cycle, 584–586,
585F
Regulators of G-protein signaling, 1038
Regulatory enzyme
definition of, 383D
nonlinear Lineweaver–Burk or

Hanes–Woolf plots, 395
Reg
ulatory gene, 914–915
Regulatory protein, 913
gene, 935–939, 939F
Relaxed DNA, 334
Relaxed form of hemoglobin subunits, 473
Release factor, 974
Remodeling, bone, 282–283
Renaturation of DNA, 331–332
Rep helicase, 500
Repair
of DNA, 887–891, 890F, 892F
of genetic deficiency, 376, 377, 378B
Repeat, inverted, 327, 328F
Replacement therapy, gene, 376, 377
Replication, DNA, 862–876. See also DNA,
replication of
Replication activator protein, 872
Replication factory, 870
Replication fork, 863, 868–869
Replication licensing factors, 872
Replication switch, 872
Replicator, 355
Reporter gene, 371
Repressible operon, 918
Repression, 452, 914D
Repressor
lac, 915–916, 915F, 917B, 917T
Trp, 920

Repulsion, electrostatic, 60, 61F
Reserpine, 1054B–1055B
Residue
amino acid, 89, 433B
in alpha-helix, 139
hydroxylated
of collagen, 150F
of proline, 150S
invariant, 113
sialic acid, 208S
Resistance, drug, 283, 285
Resonance
competing, 60
peptide bond, 87, 89, 136
stabilization of hydrolysis products by
, 60
Resonance-stabilized carbanion intermedi-
ate, 711F
Respiratory acidosis, 44B
Respiratory alkalosis, 44B
Response element, 927, 928–929
cAMP, 936B
Restriction endonuclease, 310–313, 311T,
312F, 313
Restriction endonuclease EcoRI, 356F
Restriction enzyme, 310–313
Restriction fragment size, 312–313
Reticulum
endoplasmic, 20
of animal cell, 23T

of plant cell, 24T
signal peptidase and, 996–997
sarcoplasmic, 280
Retina, docosahexaenoic acid in, 736B
Retinal, 285S
Retrograde translocation, 997
Retrovirus, 876B
Reunion of DNA strands, 877–878
Reverse transcriptase, 363, 876–877
Reverse transcriptase polymerase chain
reaction, 373
Reverse transcriptase-driven synthesis of
cDNA, 366F
RF, 974
RGS proteins, 1039, 1039F
Rhamnogalacturonan II, 199B
␣-
L-Rhamnose, 189S
Rho termination factor, 912
Rhodopseudomonas viridis photosynthetic
reaction center, 642–645, 642F,
643F, 643G
Rhodopsin, 252F
Ribbon, extended, 197
Ribbon structure of protein, 156F
Ribitol, 189
Ribitol phosphate, 204
Riboflavin, 524T
␤-
D-Ribofuranose, 295

Ribonuclease
bovine, 152
unfolding of, 161F
Ribonuclease A, 94F, 152F, 152G
size of molecule of, 90T
Ribonucleic acid. See mRNA; RNA
Ribonucleoprotein particle, 941
small nuclear, 305
Ribonucleotide, 294F, 295D
Ribonucleotide reductase, 831–832, 832F
D-Ribose, 186S
Ribose zipper, 344
Ribose-5-P, 691–692
␣-
D-Ribose-5-phosphate, 189F
Ribose-5-phosphate pyrophosphokinase, 814
Ribosomal protein, 962
Ribosomal RNA, 299, 303–304, 304F, 305F,
306, 962–963, 963F
intrastrand base pairing and, 346, 348
Ribosomal subunit, 974, 976F
Ribosome
assembly of, 961–965
catalytic power of, 970–971
definition of, 961D
eukaryotic, 305F, 964–965, 965F
life cycle of, 976F
in plant cell, 24T
prokaryotic, 305F, 962–963
prokaryotic cell, 20T

spontaneous self-assembly of, 963
structural organization of, 961–965,
962T, 963F, 965T
translocon and, 995
tRNA-binding sites on, 966F
Ribosome binding site, 967
Ribosome nascent chain:SP complex,
995–996
Ribosome recycling factor, 974
Ribosome RNA
secondary structure of, 349F
tertiary structure of, 349F, 349G
Riboswitches, 350
Ribothymidine, 305S
Ribothymidylic acid, 304
Ribozyme, 410–412, 411F
Ribulose, 90T
D-Ribulose, 183S
Ribulose bisphosphate, 651
Ribulose bisphosphate carboxylase, 656
Ribulose-1,5-bisphosphate, 651, 651G
Ribulose-1,5-bisphosphate carboxylase reac-
tion, 651
Ribulose-5-phosphate kinase, 653
Rieske protein, 169F, 604
Right-handed DNA, 323, 324F
Ring
furanose, 187
purine, 292F
pyrimidine, 292F

Ritonavir, 443S
RLFs, 872
RNA
biological significance of, 307
of cloned genes, 369–372, 369F, 370F
definition of, 297D
double-stranded, 375
eukaryotic transcript, 305
hydrolysis of, 307
messenger. See mRNA entries
micro, 306
noncoding, 306
ribosomal, 303–304, 304F, 305F, 306
intrastrand base pairing and, 346, 348
operons of, 963F
ribozymes, 410–412, 411F
secondary structure of, 341–350, 345F,
345S, 346S, 347S, 348F, 349F
small, 305, 306
small interfering, 375
splicing of, 944
transfer, 304–305
unusual bases of, 305S
vincinal -OH groups of, 308F
RNA editing, 945–946
RNA enzyme, 411–412, 412F
RNA expression, 369
RNA genome, replication of, 876–877,
876B
RNA interference, 375

RNA polymerase
in eukaryotes, 924–925, 925G, 926T, 930
I, 924
Index I-29
II, 924, 925G, 926T
III, 924
in prokaryotes, 908, 909F, 910–911
RNA polymerase holoenzyme, 906–907
RNA-directed DNA polymerase activity, 876
RNA-induced silencing complex, 375
RNase, 309
RNase H, 876
RNase PH, 947
RNC-SRP, 995–996
Robinson, Sir Robert, 753B
Rosanoff, M.A., 82B
Rosanoff convention, 82B
Rossman fold, 501
Rotating molecular motor, 481
Rotation
of flagella, 503–504
optical, 80
Rotation axis, twofold, 174
Rotenone, 617S
Rough endoplasmic reticulum, 21F
Rous sarcoma virus, 1023
RRF, 974
rRNA, 962–963, 963F
(R,S) system, 81–82, 84B
R-SNARE, 269

RT-PCR, 373
Rubisco, 651
Rubisco activase, 652
Rule, Chargaff’s, 300T
RuvA, 880, 883–885
RuvB, 880, 883–885
RuvC, 880, 883–885
RuvC resolvase, 885
70S complex, 974
48S initiation complex, 979F
80S initiation complex, 979
43S preinitiation complex, 977F, 978
20S proteasome, 1000
26S proteasome, 1000, 1000G
19S regulator, 1000
70S ribosome:RF1:RF3-GTP:termination
signal complex, 974
Saccharide, 204, 205S, 206F
Saccharopine, 787
Saccharopine pathway, 809
SAGA complex, 933
SAICAR synthase, 815F
Salivary ␣-amylase, 196
Salmonella, 204
Salt, bile, 700
Salt bridge between subunits of hemoglo-
bin, 473F
Salting-in of protein, 98
Salvage of purines, 821, 821F
SAM, 790, 997–998

Sample half-cell, 594
Sanger, F., 316
Sanger’s chain termination, 317–320
Saponification, 222
Saquinavir, 425B, 443S
Sarcolemma, 483
Sarcoma virus, Rous, 1023
Sarcomeres, 483
Sarcoplasmic reticulum, 280, 483
Sarin, 1051S, 1052
Saturated fatty acid, 219D
Saturation behavior, 271
Saturation curve, 122, 122F
oxygen, 474F
substrate, 389
Saturation effect, 389
Saxitoxin, 1049B
Scaffolding proteins, 266–267
Schiff base linkage, 285S
Schizosaccharomyces pombe, 845
Schönbein, Christian, 201B
Schultze, Major E., 201B
SCID, 378B, 822B
SCOP, 158
Scramblases, 262
Screening of DNA library, 362, 362F, 370
Scurvy, 155B
SDS-PAGE, 131
SDS-polyacrylamide gel electrophoresis,
130–131

Seawater, 5T
Sec61 complex, 996
SECIS element, 954B
Second genetic code, 953, 955
Second messenger
calcium as, 1031
cyclic AMP as, 466, 1025–1026, 1026F,
1026G, 1026T
intracellular, 1026T
phosphatidylcholine generating, 1031
released by phospholipase, 1028
Secondar
y active transport, 286–287
Secondary structure
of DNA, 320–333. See also DNA, sec-
ondary structure of
of proteins, 136–146. See also Protein,
secondary structure of
of RNA, 341–350, 345F, 345S, 346S,
347S, 348F, 349F
Second-order reaction, 387
Secreted polypeptide hormone, 1010
Secretion
insulin, 680
of pancreatic juice, 699F
retrograde translocation preventing,
997
Secretory protein, 995
Sedimentation coefficient, 132–133, 303
Sedoheptulose-1,7-bisphosphatase, 653

Selectable marker, 355
Selectins, 213T, 214, 214F
Selectivity filter, 272, 274
Selenocysteine, 75S, 954B
Self-replication, 3–4
Self-splicing, 411
Sensor, 923
Separation, protein, 97–98, 98B
Sequence
consensus, 908D, 928T
DNA
cloning of, 355–356, 356F
gene regulatory proteins and,
935–939, 939F
insertion, 886
intervening, 303
nucleic acid, 907B
signal, 994
stop-transfer, 997
upstream activation, 927
Sequence tag, expressed, 366
Sequence-specific transcription factor, 937
Sequencing
amino acid, 100–110. See also Amino
acid sequencing
DNA, 318F
automated, 318–320
genome, 17–18
Sequencing gel, dideoxy, 318–320
Sequential reaction, 403

Serglycin, 210F
Serine
catabolism of, 804
ethanolamine and, 741
in green fluorescent protein, 81B
in lipid synthesis, 741
pK
a
value for, 77T
sphingolipid synthesis and, 744–745
structure of, 72S
synthesis of, 793, 796F
Serine acetyltransferase, 795
Serine dehydratase reaction, 807B
Serine hydroxymethyltransferase, 816B
Serine phosphatase, 793
Serine protease, 434, 436F, 437, 438F, 439B
Serotonin, 75S, 76
Serpin, 171B
Serum albumin, 90T
Serum cholesterol, 761
Seryl tRNA synthetase, 148B
Sesquiterpene, 229, 230S, 231
Severe combined immunodeficiency syn-
drome, 378B, 822B
Sex hormone, 763
SH modification in cleavage of disulfide
bridges, 102F
Sheet
␤. See Beta sheet

in globular proteins, 152–153, 152G,
154G
parallel, in proteins, 143
Shift
chemical, 83–84, 85F
hyperchromic, 330
keto-enol tautomeric, 293
Shikimate pathway, 793, 799F
Shine-Dalgarno sequence, 967, 967F
Short-chain acyl-CoA dehydrogenase, 705
Shuttle, malate–aspartate, 621
Shuttle vector, 360, 360F
Sialic acid, 191S, 208S, 228
Sickle cell anemia, 476–478
Side chain, amino acid, 78–79
Sigma factors, 907
Sigmoid curve, 456
Signal
GPCR, 1024–1025
polyadenylation, 940
Signal peptidase, 994, 996–997
Signal peptide, 996
Signal receptor, 994
Signal recog
nition particle, 994, 995
Signal sequence, 994
Signal transduction pathway, 257, 992–993,
1010–1013, 1012F
Signal transduction unit, 1025
Signalsome, 1011

Signal-transducing receptor, 1012F–1013F,
1013–1024, 1013G, 1024B
Silencer, 927
Silencing, gene, 306–307
I-30 Index
Silk, spider, 144
Silk fibroin, 149F
Simple protein, 119
Simple sugar, 181D
Singer, S. J., 245
Single polycistronic mRNA, 912–913
Single transmembrane segment, 249–250,
249F
Single-displacement bisubstrate mecha-
nism, 403F
Single-displacement reaction, 403, 403F,
405–406
Single-strand assimilation, 882–883
Single-stranded DNA
damage, 887
description of, 331
Single-stranded DNA-binding protein, 863
siRNA, 306
Siroheme, 770
Site
active, 389, 398
catalytic, 178
cloning, 355
substrate-binding, 398
Sitosterol, 236S

Size exclusion chromatography, 130–131
Skeletal muscle, 481–490. See also Muscle
contraction
energy metabolism of, 848T
metabolic role of, 849–851, 850B
structure of, 482F
Skeletal muscle troponin T isoform, 945
Sliding filament, 486, 487F, 488–490
Slow-twitch muscles, 708B
Small interfering RNA, 306, 375
Small intestine, 699F
Small nuclear ribonucleoprotein particle,
306
Small RNA, 306
SMC proteins, 338–339, 339F
SMC1/SMC3 heterodimers, 339
SMC2/SMC4 heterodimers, 339
Smooth endoplasmic reticulum, 21F
Smooth muscle effectors, 482B
Snake venom, 235B, 308F
SNARE, 268–269, 269F
snRNP, 305, 943
Soap, 222
Sodium, action potential and, 1044–1046,
1045F, 1046
F
Sodium channel toxin, 1049B
Sodium ion
hydrolysis of ATP and, 64
secondary active transport and, 286

Solar energy. See Light energy
Solid phase oligonucleotide synthesis, 341F
Solid-ordered state, 262
Solid-phase synthesis, of peptide, 118F
Solubility, of globular protein, 98F
Soluble protein, unfolding of, 55, 55F
Solute
colligative properties and, 33–34
polar, 31
water properties and, 33
Solution, double helix in, 327
Solvent, water as, 30–34, 44
Soma, 1044
Somatic recombination, 877
Somatostatin, 1009F
Sorbitol, 189
D-Sorbose, 183S
Sorting and assembly complex, 997–998
Southern, E. M., 364B
Southern blotting, 364B
Southern hybridization, 362–363
Space
intermembrane, 592
thylakoid, 631
Specialization, organ, 847, 848F, 848T,
849–853, 851B, 851F
Specific acid–base catalysis, 430
Specific activity, 393
Specific linking difference, 335
Specificity

definition of, 383
enzyme, 383
Specificity site of ribonucleotide reductase,
832–833
Spectrin, 265
Spectrometry
amino acid properties, 82–85
mass, 105–109, 106T, 107F–108F, 109F
Spectroscopy, nuclear magnetic resonance,
526–527, 527F
Spectrum, absorption, of nucleic acid
bases, 293–294, 293F
Spermaceti, 229B
Sphingolipid, 227–229, 228F, 737, 744–745,
745F
Sphingomyelin, 227, 746F, 1031
Sphingomyelinase, 1031
Sphingosine, 227
Sphingosine-1-phosphate, 235
Spider web, 144
Spirogyra, 632F
Spliceosome, 943, 943F
Splicing, 411F, 939–940
nuclear pre-mRNA, 940–941
protein, 896B
Splicing reaction, 942–943
Split gene, 939–940
Squalene, 230S, 231, 752, 753, 754F
Squalene monooxygenase, 757
SRP, 995

SRs, 994
SSB protein, 863
S-shaped curve, 456
Stability of quaternary structure, 177
Stabilization
of hydrolysis products, 60
transition-state, in serine protease, 439B
Stacking
, coaxial, 344
Standard reduction potential, 59T
Standard state, 50
Standard-state free energy, 54–55
Standard-state free energy change, 53
Stanozolol, 764, 764F
Staphvax, 207B
Staphylococcal protease, 103
Starch, 195–196, 196S
catabolism of, 673–674, 673F
Starch phosphorylase, 195
State function, 49
Statins, 424B, 755B
Statistical thermodynamics, 51
Stator, 612
Steady state, 2
Steady-state assumption, 390
Stearic acid, 6F, 219, 220T, 221G, 221S,
222G, 222S
Stearoyl-CoA desaturase, 734
1-Stearoyl-2-oleoyl-phosphatidylcholine,
226, 226F, 226G

Steitz, Thomas, 870B
Stem-loop structure, 342, 912
Stereochemistry
of amino acid, 79–82
of monosaccharides, 183–184
Stereoisomer, 83B
Stereospecificity in NAD
ϩ
-dependent dehy-
drogenase, 579B
Steroid
anabolic, 764, 764F
cardiotonic, 280, 280G, 280S, 282B
structure and function of, 233, 234F,
234S, 236B, 238S
Steroid hormone
action of, 1008–1009
definition of, 1008D
synthesis of, 762–764
Stigmastanol, 236S
Stoeckenius, Walther, 616
Stoichiometry, 841–843, 841D
Stomata of desert plant, 659
Stop-transfer sequence, 997
Stop-transfer signal, 994
Storage, long-term memory, 936B
Storage granule, 20T
Storage polysaccharide, 194
Stored metabolic fuel, 698T
Strain, structural, 422

␤-Strand, 95F
Strand exchange, 879
Streptococcus lividans, 274, 274F
Streptomycin, 194F, 983S
Stroma, 631
magnesium ions moving into, 656
Strong electrolyte, 46
Structural complementarity, 14, 14G
Structural gene, 914–915
Structural genomics, 172B
Structural polarity, 10
Structural polysaccharide, 196–201
Structural strain, 422
Strychnine, 1053
Substrate
binding of, 389
definition of, 383
of gluconeogenesis, 662, 672–673
in glycolysis, 554–558, 556F, 558B
leadin
g, 405
obligatory, 405
suicide, 401–403
Substrate saturation curve, 389
Substrate specificity site, 831, 832–833
Substrate-binding site, 398
Substrate-level control mechanism in gluco-
neogenesis, 669–671, 671F
Substrate-level phosphorylation, 575–576
Subunit

cytochrome, 642F
of E. coli polymerase III homoenzyme,
867T
identical, dimer of, 441
of prokaryotic ribosomes, 961–962
protein, 95, 173
Succinate
oxidation of, 601–603, 602F
structure of, 150S
in TCA cycle, 576
Index I-31
Succinate dehydrogenase
competitive inhibition and, 399–400,
400F
as FAD-dependent, 576
Succinate dehydrogenase reaction, 576
Succinate thiokinase, 575
Succinate-coenzyme Q reductase, 598
N-Succinyl-5-aminoimidazole-4-carboxamide
ribonucleotide, 815F
Succinyl-CoA
amino acid catabolism and, 807
oxidation of, 711F, 712
Succinyl-CoA synthetase, in TCA cycle,
575–576
Sucrose, 192F, 192G, 192S, 193, 408
Sugar
amino, 190
deoxy, 189
simple, 181D

structure of, 10S
Sugar acid, 187–188, 188S
Sugar alcohol, 189, 189S
Sugar code
description of, 213
lectin translation of, 213
Sugar ester, 189, 189S
Sugar nucleotide, 675, 675G, 675S
Suicide substrate, 401–403
Sulfate
assimilation of, 797F
sulfide synthesis from, 796–797
Sulfatide, 228
Sulfide synthesis, 796–797, 797F
Sulfite oxidase, wild-type, 396B
Sulfmeturon methyl, 801B
Sumoylation, 933
Supercoil, 333–336, 335F, 336F, 911F
Superfamily, 158, 499, 499T, 500F
Superhelix density, 335
Suppressor tRNA, 960–961
Supramolecular complex, 6, 8F
membrane as, 9
membrane-spanning, 638
virus as, 21–22
Surface tension, of water, 45
Switch
membrane protein as, 256–258, 257B,
258F, 260
replication, 872

Symmetry, 174
Symmetry model, 457–459
Symport, 286
Synapse, 1044, 1046–1047
Synapsis, chromosome, 879, 879F
Synaptic bulb, 1044
Synaptic cleft, 1044, 1048, 1050
Synaptic junction, 1052
Synaptic knob, 1044
Synaptic terminal, 1044
Synaptotagmin, 269
Synchrony, 204
Syndecan, 209–210, 210F
Synechococcus elongatus,
644–645, 644F
Synonymous codon, 953
Synthesis
amino acid, 779–810. See also Amino
acid synthesis
of ATP, 611–620, 614F, 616F–617F, 618F,
619B, 619F
of cDNA, 366F
cholesterol, 750–757
dehydration, 191
DNA, deoxyribonucleotide formation in,
830–833, 831F, 833F
of eicosanoids, 747–750
fatty acid, 722–737. See also Fatty acid
synthesis
of fructose-2,6-bisphosphatase, 672F

of gene, 340
glycogen, 675–677, 675G, 675S, 676F,
680–683
of hexose, 647–648, 653, 655
of hybrid protein, 371F
lethal, 834B
macromolecular
, 839–840
of nucleic acid, 339–340
polypeptide, 118F, 119
protein, 952–986. See also Protein
synthesis
of pyrimidines, 826–830, 827F, 828F
of secretory proteins, 995
solid phase oligonucletotide, 341F
of thymine nucleotide, 833–836, 834B,
835B, 836F
Synthesis method, primed, 317
Synthetase
Acyl-CoA, 702
arginosuccinate, 784
glutamine, 774, 775F
regulation of, 776–779, 777F, 777G,
778F
Synthetic combinatorial library, 361B
Synvinolin, 755B
Szent-Györgyi, Albert, 488
T lymphocyte, 897
Tabun, 1051S, 1052
TAF, 930

Tag, expressed sequence, 366
D-Tagatose, 183S
Tail, myosin, 484
D-Talose, 182S
Tamiflu, 425B
Tandem enzyme, 671
Tandem mass spectrometry, 107–108,
109F
Tangle, neurofibrillary, 988B
TATA box, 927, 927F
Taurocholic acid, 761F
Taut form of hemoglobin subunits, 473
Tautomeric shift, keto-enol, 293
Taxol, 494B
TBP, 930
Teichoic acid, 204
Telomerase, 875
Telomere, 299D, 340B, 874, 875B, 875F
Temperature
enzymatic activity and, 397, 397F
melting, 331
of water, 44–45
Template, 317
DNA, 862, 862D
Template DNA, 908, 910–911
Template strand, 907B
Tense form of hemoglobin subunits,
473
Ter region, 869–870
Terminal, synaptic, 1044

Terminal chain segment, glycogen,
677–678, 678F
Termination, 966
peptide chain, 974, 975F
in eukaryotes, 981
in protein synthesis, 974, 975F
Sanger’s chain, 317–320
Termination codon, 953
Termination site, 912
Terminator, 922
Terpene, 229–232, 230S, 231B, 231S, 232B
Tertiary structure
of DNA. See also DNA, tertiary structure
of
of protein, 95, 146–172. See also Protein,
tertiary structure of
of rRNA, 348, 349G
of transfer RNA, 345, 346F, 348
Testosterone, 233, 234S, 238S, 1009F
Tetracycline, 983S
Tetrahedral oxyanion transition state, 439B
Tetrahydrofolate, 816B
Tetraloop, 343
Tetrodotoxin, 1049B
Tetrulose, 183
TF, 988
TFII, 930, 933
TFIII, 925
Therapy, gene, 376, 377, 378B
Thermal cycler, 373

Thermal denaturation, of DNA, 330–331,
333F
Thermal properties of water, 44–45
Thermoacidophile, 19
Thermodynamic parameters for protein
denaturation, 51T
Thermodynamic potential, 66, 382
Thermodynamics, 48–69
ATP hydrolysis and, 64
coupled processes and, 66
electron transport and, 611
enthalpy and, 49–51
first law of, 48–49
of glycolysis, 538T
high-energy biomolecules and, 56, 57T
parameters of, 55–56
pH and, 54–55
requirement for ATP and, 66
second law of, 51–52
third law of, 52
Thermogenin, 619B, 852
Thiamine, 524T
Thiamine pyrophosphate, 350F, 568B
Thick filament, 484–485
Thin filament, 483F, 484
Thioester
-linked fatty acyl, 257
Thioether-linked prenyl, 257
Thiokinase, fatty acid, 702
Thiolase, 707, 752–753

Thiolase reaction, 707F
Thioredoxin, 831–832
Thioredoxin reductase, 831, 832
4-Thiouridine, 305S
Third-base degeneracy, 953
Threonine, 790, 791F
pK
a
value for, 77T
stereoisomers of, 83B
structure of, 73S
synthesis of, 790, 791F
Threonine deaminase, 793
Threonine synthase, 790
D-Threose, 182S
I-32 Index
Thrombin, 113
Thromboxane, 747
Thylakoid lumen, 631
Thylakoid membrane, 631
Thylakoid space, 631
Thylakoid vesicle, 631, 656
Thymidine, 294
Thymidylate synthase, 169F, 835, 836F
Thymidylate synthase reaction, 836F
Thymine, 292, 292F, 301S
Thymine nucleotide synthesis, 833–836,
834B, 835B, 836F
Tight turn in protein, 145
TIM, 998

TIM barrel, 159
Titration, 78F, 79F
Titration curve, 39
7-TMS protein, 1015
TMS receptor, 1015
Toluene, 56
TOM, 997
Tomography, positron emission, 555B
Top-of-power stroke, 489
Topoisomerase, 334
Topology, supercoil, 333–334
Total adenine nucleotide pool, 843–844
Toxic shock syndrome, 227B
Toxin
diphtheria, peptide chain termination
in, 980B
tetrodotoxin, 1049B
TPP-dependent transketolase reaction, 689F
Tracer, isotopic, 525–526, 525T, 526F
TRAM, 996
Transaldolase, 689–690, 690F
Transamination of pyruvate to alanine,
851F
Transamination reaction, 782B
Transcarboxylase, 724
trans-complex, 269
Transcriptase, reverse, 363
Transcription, 906–951
DNA, 291, 292F
eukaryotic, 305, 924–925, 925G, 926T

initiation of, 931F, 931G
Mediator effects on, 932
in prokaryotes, 906–912, 909F, 910B,
911F, 913F
regulation of, 912–923, 914F, 915F,
916T, 917B, 918F, 918G, 919F,
921F, 922F
steroid hormones and, 763
supercoiling vs., 911F
Transcription activator, 934
Transcription attenuation, 920
Transcription factor, 924
CREB-type, 936B
general, 929
heat shock, 929
sequence-specific, 937
Transcription start site, 908
Transcriptional activator, 923
Transcriptome, 367D
Transcriptomics, 513
Transduction
energy, 522, 636
of GPCR signals, 1024–1025
Transduction pathway, 1031F
signal, 257, 1010–1013, 1012F
Transfer, peptidyl, 969
T
ransfer potential
group, 58–59
types of, 59T

Transfer protein, cholesterol ester, 758
Transfer RNA. See tRNA
Transferase
adenylyl, 777
peptidyl, 964, 969
phosphoethanolamine, 741
Transformation experiment, bacterial, 359F
Transforming growth factor ␤, 212
Transgenic animal, 889B
Trans-hydration of fumarase, 577
Transient receptor potential, 275
Transition state, 387, 419
tetrahedral oxyanion, 439B
Transition-state analogs, 423, 424B–425B
Transition-state stabilization, in serine pro-
tease, 439B
Transketolase, 688–689, 688F
Translation, 291, 292F
Translocase
acylcarnitine and, 702
ATP–ADP, 618, 619F
Translocases, 498
Translocation, 964, 969
protein, 994
retrograde, 997
Translocon, 996
Transmembrane segment, single, 249–250,
249F
7-Transmembrane segment protein, 1015
Transpeptidation, 969

Transport
electron, 592–629. See also Electron
transport
membrane, 260, 269–287. See also
Membrane, transport across
Transposable element, 886
Transposition, 877, 886
Transposon, 886, 886F
Transverse asymmetry, 260–261
Transverse tubules, 483
Tranylcypromine, 1055B
Treadmilling, 490
Trehalose, 193B
Triacylglycerol, 737, 757–758
energy stored as, 697
fatty acids liberated from, 698F
structure and function of, 222, 222G,
222S, 223
Triacylglycerol lipase, 700
Triage, protein, 1004B
Triantennary oligosaccharide, 209
Tricarboxylic acid cycle, 532B, 563–591
aconitase reaction in, 573, 573F, 573G
chemical logic of, 564
citrate synthase in, 571–574, 571F, 572G
diagram of, 565F
energetic consequences of, 578–581
enzymes and reactions of, 572T
fluoroacetate blocking, 573–574
intermediates in, 581–582

isocitrate dehydrogenase in, 574, 574F,
574G
isocitrate formation in, 572–574
␣-ketoglutarate dehydrogenase in, 575
overview of, 563–564, 564F
oxaloactetate and, 575–578
oxidation of succinyl CoA and, 712
pyruvate and, 566
pyruvate dehydrogenase complex in,
571F
regulation of, 584–586, 585F
Trigger factor, 988
Trioleoylglycerol, 222
Triose, 183
Triose kinase, 555
Triose phosphate isomerase, 159F, 394T
backbone structures of, 167F
in glycolysis, 544, 545F,
545G
T
riple helix of collagen, 150–151, 151F, 151S
Triplet code, 952–953
Tristearin, 222G, 222S
Tristearoylglycerol, 222
Triterpene, 230S, 231
Triton X-100, 245S
tRNA, 299, 304–305
aminoacyl-tRNA synthetase recognizing,
956–958
cognate, 955

intrastrand base pairing and, 344–345
structure of, 953S
general, 953F
secondary, 345
tertiary, 345, 346F, 348
suppressor, nonsense codons and,
960–961
tRNA
Ala
, 958
tRNA-binding site, 966F
tRNA
i
Met
, 977
Trojan horse substrate, 402
Tropocollagen, 150
Tropomyosin, 483D
Troponin, 483D
Troponin C, 849, 1031
Troponin T isoform, muscle, 945
trp operon, 914, 920
trp repressor, 920
Trypsin
naming of, 384
in polypeptide fragmentation, 103, 104F
as serine protease, 113
trypsinogen, 434, 435F
Tryptophan
pK

a
value for, 77T
structure of, 73S
synthesis of, 799–802, 800F, 802G
ultraviolet light absorbed by, 82
Tryptophan synthase, 802, 802F, 802G
d-Tubocurarine, 1050
Tubulin, 490
Tumor. See also Cancer
positron emission tomography of, 555B
telomeres and, 340B
Tumor-suppressor gene, 1029B
Tunneling, 433B, 802
Turnover number, 393, 393T
Tus protein, 870
Twist, 334
helical, 323F
propeller, 323, 323F
Two-dimensional gel electrophoresis,
131–132, 131F
Twofold rotation axis, 174
Two-state transition, 160
Tyk2, 1037
Index I-33
Type 1 diabetes, 717B
Type 2 diabetes, 717B
Tyrosine
catabolism of, 809–810, 809F
catecholamine transmitters derived
from, 1056

in green fluorescent protein, 81B
pK
a
value for, 77T
structure of, 73S
synthesis of, 798–799, 800F, 801F
ultraviolet light absorbed by, 82
Tyrosine hydroxylase, 1056
Tyrosine kinase, 1015
nonreceptor, 1023–1024
phospholipase C activation by, 1030
Tyrosine kinase pp60
c-src
, 1036, 1036F
Tyrosine kinase pp60
v-src
, 1023
Tyrosine kinases, 461
Ubiquinone, 598
Ubiquitin, 998
Ubiquitin-activating enzyme, 998
Ubiquitination, 998
Ubiquitin-carrier protein, 998
Ubiquitin-protein ligase, 998
UCP1, 619B
UDP–glucose pyrophosphorylase, 556,
557F, 676, 676F
UDP–glucose-4-epimerase, 556
Ultracentrifugation, 132–133
Ultrafiltration, 129

Ultraviolet light
amino acid absorbing, 82
denaturation of DNA and, 330
pyrimidine dimer repair and, 890
pyrimidines and purines and, 293, 293F
UMP synthase, 828
Uncharged amino acid, 74
Uncompetitive inhibition, 401
Uncoupler, 618, 619B
Uncoupling protein-1, 619B, 852
Undecaprenyl alcohol, 231S
Unfolded protein, natively, 168
Unfolding of protein, 55
Unilamellar vesicle, 244F, 245
Unsaturated fatty acid, 219D, 733–734
oxidation of, 713–714
Unstructured protein, 168
Unwinding of helix, 863
Upstream, 908
Upstream activation sequence, 927
Uptake, single-strand, 883
Uracil, 292, 292F, 307S
Urate oxidase, 825
Urea, 810
Urea cycle, 783, 785, 786F, 787, 787B
Urease, 420T, 826
Urease reaction, 419
Ureido group, 784
Ureotelic, 810
Uric acid, 293S, 810, 813

gout caused by, 824–825
purine catabolism and, 823
structure of, 814S
Uricotelic organism, 810
Uridine, 294, 295S
Uridine 5Ј-diphosphate, 296
Uridine diphosphate glucose, 675G, 675S,
676
Uridine diphosphoglucose, 57
T
Uridine 5Ј-monophosphate, 296S
Uridylic acid, 295
Uridylylation, 461T
Uroguanylin, 1021
Uronic acid, 188
UTP, UMP synthesis and, 829
U-turn, 343
Vacuolar ATPase, 282
Vacuole, 20, 24T
Vacuum blotting, 364B
Valine
catabolism of, 807, 808F
pK
a
value for, 77T
structure of, 72S
synthesis of, 793, 794F
van der Waals contact distance, 12
van der Waals forces, 12, 12F
van der Waals interaction

description of, 11T
DNA and, 321–322
ubiquitousness of, 136
van der Waals interaction energy, 12F
Vancocin, 207B
Van’t Hoff plot, 50
Vaporization, 44
Variable loop, 345
Vasoactive intestinal peptide, 1056
V(D)J recombinase, 900–902
Vector
cloning, 355, 355F
expression, 369, 369F, 370F
expression-cloning, 370F
plasmid, 356F
shuttle, 360, 360F
Vein, portal, 680, 680F
Velocity
of enzyme-catalyzed reaction, 386
in Michaelis–Menten equation, 390–391
Venom, snake, 308F
Versican, 209, 210F
Very long-chain acyl-CoA dehydrogenase,
704–705, 705F
Very-low-density lipoprotein, 757, 758
Vesicle
coated, 758
multilamellar, 244F, 245
thylakoid, 631, 656
unilamellar, 244F, 245

Vesicle-mediated transport, 268F
Vevesca, 207B
VH gene, 900
Viagra, 404B, 404S
Viceroy butterfly, 282B
Vicinal XOH groups of RNA, 308F
Vinblastine, 284F, 494B
Vinca alkaloids, 494B
Vincristine, 284F, 494B
Viracept, 443S
Viral neuraminidase inhibitor, 425B
Viral transforming protein, 1023
Virus, 876B
in g
ene delivery system, 377, 378F
Rous sarcoma, 1023
structure and function of, 21–22, 24F–25F
Vitamin B
12
activation of, 712B
catalysis of, 711–712
Vitamin C deficiency, 155B
Vitamin K epoxide reductase, 232B
Vitamin K reductase, 232B
Vitamins, 523, 524T
Vitellogenin gene, 940
VLDL, 757, 758
Voltage-dependent anion channel,
624
Voltage-gated ion channel, 1044

von Gierke disease, 681B
V-type ATPase, 1050
Walker, John, 613
Wall, cell, 19, 20T
bacterial, 201–204, 202S, 203F
of plant cell, 24T
Warburg, Otto, 535
Warfarin, 232B
Water, 28–47
buffers and, 41–44
environmental role of, 44–45
lipid structures formed in, 244–245,
244F, 245S
metabolic, 710
pH and, 35–40, 36T
properties of, 28–35
colligative, 33–34
forming ions, 34–35
hydrogen bonding as, 29–30
solvent, 30–34
unusual, 28
structure of, 29S
Water:plastoquinone oxidoreductase,
638
Watson, J. D., 862
Watson–Crick base pair, 321
Watson–Crick postulate of double helix,
301, 301F
Wavelength, 634
Wax, 229, 229B, 230S

WD40 repeat domain, 625
Weak acid, polyprotic, 76–78
Weak electrolyte, 37
Weak force
chemical, 11, 11T
biomolecular recognition and,
14–15
environmental conditions and, 15
quaternary protein structure and, 174,
176
Web, spider, 144
Western blotting, 364B
Wheel, helical, 153, 1033, 1033F
Whole genome sequencing, 17–18
Wild-type human sulfite oxidase, 396
B
Wobble hypothesis of codon–anticodon
pairing, 959
Woodward, R. B., 753B
Work, mechanical, 49
Writhe, 334
Wyman, Jeffries, 457
Wza, 256
Xanthine, 293S
Xanthine oxidase, 823–824, 825F
Xylitol, 189
␣-Xylosyl-threonine, 205S
D-Xylulose, 183S
Xyluose-5-phosphate, 692–693, 692F
I-34 Index

YAC, 360
Yeast
enolase, 550F
hexokinase, 540F
phenylalanine tRNA, 346F, 347F, 347G
RNA polymerase II subunits of, 926T
rRNA of, 348F
Yeast artificial chromosome, 360
Yeast mating factor, 260
Yeast two-hybrid system, 372–373, 372F
Z line, 483
Z scheme, 638, 639F, 640
Z-DNA, 323–324, 324F, 325T, 326
cytosine methylation and, 326
Zero-order kinetics, 389
Zinc finger, 936, 937F
Zipper, ribose, 344
Zipper motif, 938
Zn finger motif, 937–938, 937F
Zn-finger, 936, 937F
Z-variant of protein, 171B
Zwitterion, 70D, 76F
Zymogen, 434
as enzyme precursor, 454–455,
454F–455F, 454T
gastric and pancreatic, 454–455, 454T