Legislación según la cual se han creado los valores

glucosyl transferase role, 739, 739F misfolded proteins, 739–741, 740F molten globule, 387–388, 388F monitoring, 738–739

N-linked glycosylation role, 737F, 747F noncovalent interactions, 64, 64F, 126–127, 130F pathways, 388F

prion proteins, 1498–1499 see also Prion proteins (PrP) quality control, 390–391, 391F, 767–768 refolding, 131, 131F, 391, 391F

see also Chaperones relation to synthesis, 387 Protein function, 152–196

enzymes see Enzyme(s)

phosphorylation effects see Protein phosphorylation

protein–ligand binding see Protein–ligand interactions

structure–function relationship, 154–155 Protein glycosylation, 388F, 736–738, 737F, 747F

see also Endoplasmic reticulum (ER) Protein identification, 519–532

mass spectrometry, 519–521

see also Protein analysis; Protein purification Protein interaction maps, 188–190, 189F, 190F Protein kinase(s), 176–178, 895 Cdk inactivation, 1063–1064, 1064F, 1066T evolution, 176, 177F regulation, “microchips,” 177–178, 177F, 179F sequence homology, 176, 177F structure, 141, 176F

tyrosine kinases see Tyrosine kinase(s) see also individual enzymes

Protein kinase B (Akt; PKB), 934, 1244 Protein kinase C (PKC), 185, 626, 911 Protein–ligand interactions, 153

amino acid side-chains, 154–155, 154F, 155F antigen–antibody see Antigen–antibody binding binding sites, 153, 153F, 154F, 155F

binding strength, 157–158 see also Equilibrium constant (K) cooperativity, 172–173, 173F

see also Allosteric regulation enzyme–substrate see Enzyme–substrate

interactions linkage, 171–172, 172FF

noncovalent interactions, 153, 153F, 154, 154F, 155F

regulation, 169–170

allostery see Allosteric regulation specificity, 153

water exclusion, 154

see also Protein–DNA interactions; Protein–protein interactions Protein machines, 184–186 activation, 185–186 gene minimization, 184–185 interchangeable parts, 184–185 position in cell, 185–186, 186F scaffold proteins, 184–185, 185–186 structure, 184

see also Protein complexes (assemblies) Protein microarrays, 188

Protein modules, 140–141, 175–176 Protein motifs, DNA-binding motifs see DNA-

binding motifs (proteins) ‘Protein-only inheritance,’ yeast, 398, 398F Protein phosphatase(s), 176–177, 176F, 895

Cdk activation, 1063, 1063F, 1066T, 1074–1075 5’ mRNA capping, 347F, 3446

protein tyrosine phosphatases (PTPs), 938–939 Protein phosphorylation, 175–178

ATP as phosphate donor, 84F energetics, 177

enzymes involved, 176, 176F see also Protein kinase(s); Protein

phosphatase(s)

functional effects, 175–176, 186–187, 187F gene regulatory proteins, 450, 451F GTP-GDP exchange as alternative to

phosphorylation, 178–179 GTP-mediated see GTP-binding proteins

(GTPases) phosphorylation cycles, 177

phosphorylation site as recognition signal for protein binding, 175–176 Rb protein regulation, 1104 Protein–protein interactions, 187–190 analysis methods, 523–527 dimerization, 142 interface types, 156, 156F map construction, 188–190, 524 optical methods, 524–526 quaternary structure, 136

SH2 domains see SH2 domain (Src homology 2 domain) single molecules, 526–527 subunits, 140F, 141F, 142–143, 148F Protein purification chromatography, 512–514, 515F, 535F electrophoresis, 517, 518FF, 521–522, 522FF Western blotting, 519F

see also Protein analysis; Recombinant proteins Protein sorting apical domain, 806–807 basolateral domain, 807 endosomes, 807F glycosphingolipids, 807 lipid rafts, 807 signals, 699, 701–702, 701F, 702T, 703F trans Golgi network, 807F

Protein stains, Coomassie blue, 517, 518F

Protein structure, 59–60, 125–152 amino acid sequence, 125–137

see also Amino acid(s) analysis, 139

components, 126F

computational analysis, 139, 139F

conformation, 130–131, 154–155, 154F, 155F see also Allosteric regulation; Conformational

changes core structure, 131, 135, 135F C-terminus, 59, 126F, 482–483 depicting, 132–133FF, 144F determination, 139, 517–532 SDS-PAGE, 517 X-ray diffraction, 139, 527–529, 528F domains, 131, 136, 348 3-D models, 131, 132–133FF, 137F evolutionary tracing, 155–156, 155F, 257F fusion, 560F

large kinase domain, 136F modules, 140–141, 140F paired, 141 SH2 domain, 131, 132–133FF, 136F, 155, 156 SH3 domain, 136F helical filaments, 143, 144F, 145, 145F actin, 145F

see also Actin/actin filaments assembly, 145F

electron microscopy, 610F handedness, 143

limited fold numbers, 136–137 membrane spanning regions, 135 noncovalent forces, 126–127 N-terminus, 59, 126F polypeptide backbone, 125 primary structure, 136

coding, 199–200, 199F, 200F see also Genetic code prediction, 550–551 quaternary structure, 136 secondary structure, 136 a helix, 131, 134F, 135, 135F b sheets, 131, 134F, 135, 135F, 422, 423F stability, 137, 147–148, 147F structure–function relationship, 154–155 subunits, 140F, 141F, 142–143, 143F tertiary structure, 136

unstructured polypeptide chains, 146–147 see also Peptide bonds; Protein folding Protein structure–function relationship, 154–155 Protein synthesis, 85, 85F, 366–400

elongation cycle, 373, 373F, 376F, 377F elongation factors, 179–180, 377–378, 377F peptidyl transferase, 376, 379, 379F steps, 375–376, 376F

ER and see under Endoplasmic reticulum (ER) eucaryotic, 345F, 380, 380F, 399F

evolution, 407–408

experimental analysis, cell-free systems, 512 inhibitors, 384, 385T

see also Antibiotics initiation, 379–380, 380F levels of regulation, 399 location see Ribosome(s)

peptide bond formation, 59, 60F, 125, 373F post-translational alterations see Post-

translational modification procaryotic, 345F, 380

reading frames, 368, 368F

relation to DNA see Gene expression; Genetic code; Messenger RNA

termination, 381, 381F

see also Protein folding; Translation Protein tags

affinity chromatography, 515F cleavable, 515

GST, 514–515, 516F histidine tag, 548

see also Affinity chromatography; Epitope tagging

Protein translocation, 703F

across chloroplast membranes, 719–720 see also Chloroplast(s),protein import across mitochondrial membranes, 713–718

see also Mitochondrial protein import in endoplasmic reticulum see Endoplasmic

reticulum (ER) Protein translocators, 714–715 Protein transport

across membranes, 695–748

chloroplasts see Chloroplast(s), protein import endoplasmic reticulum see Endoplasmic

reticulum (ER), protein transport gated, 700, 701F

general flow, 701F

mitochondria see Mitochondrial protein import nucleus see Nuclear–cytoplasmic transport between organelles, 699–701

peroxisomes see Peroxisome(s), protein import signal hypothesis, 726–727, 727F, 728F studies, 703F

through secretory pathway, 749–787 see also Protein sorting; Transmembrane

protein(s); Vesicular transport Protein tyrosine kinases see Tyrosine kinase(s) Protein tyrosine phosphatases (PTPs), 938–939 Proteoglycan(s), 1184T

aggregates, 1182, 1182F, 1183F

assembly/synthesis, 775–776, 1181, 1181F basal lamina, 1165

cell surface co-receptors, 1183–1184 connective tissues, 1179, 1181–1182 membrane proteins, 636

as molecular sieves, 1182–1183 protein regulation by, 1182–1183 sizes, 1181–1182, 1181F see also specific types Proteolysis, 391

apoptosis (programmed cell death), caspases see Caspase(s)

cell cycle control, 1064 degradation signals, 396F insulin, 151, 152F

protein aggregate resistance, 397 regulated destruction, 395–396, 396F regulatory function, 395–396

see also Proteasome(s); Ubiquitin pathway Proteomics, 188

Protists, 32–34, 33F Protocadherins, 1136, 1138T Protofilament, 971–972, 972F Proton see Hydrogen ion (H+_{, proton)}

Proton gradients see Electrochemical proton gradients Proton-motive force, 821, 821F, 853–854 Proton pumps, 827–828, 829F allostery, 836 atomic detail, 835 bacteriorhodopsin, 640–642 evolution, 871 general mechanism, 837F lysosomes, 780, 780F photosynthesis, 851, 854 redox potentials, 835, 835F

see also Respiratory enzyme complexes Proto-oncogenes, 1231, 1237, 1237F Protozoa, 28F, 32–33

as parasites, 1494–1495, 1508–1511 Protrusion, in cell movement, of actin meshwork at

leading edge, 1039F Prox1 protein, 1448

P-selectin, 1145–1146 Pseudogenes, 248, 255, 257 Pseudoknot, RNA structure, 403F Pseudomonas aeruginosa, 1491 Pseudopodia, 1037

Pseudouridine, transfer RNA modification, 368F P-site (ribosome binding), 375F, 376

Psychoactive drugs, 686, 690

PTB domain (phosphotyrosine-binding domain), 898, 899F, 925

PTEN phosphatase (tumor suppressor), 933 P-type pumps (ATPases), 659, 660F

see also Calcium pump; Sodium–potassium pump (ATPase)

Puberty, 1288–1289, 1292, 1293 Puffer fish (Fugu rubripes), 30, 31F, 251F Pulse-chase experiments, 602, 602F Pulsed-field gel electrophoresis, 534 Puma, apoptosis, 1123

Pumps see Carrier protein(s) Pupa, Drosophila, 1329 Purifying selection, 247 Purine base(s), 61, 116F

depurination, 296, 297F see also Adenine; Guanine Purkinje cell, intracellular calcium, 597F Puromycin, 384, 385T

Purple bacteria

mitochondrial evolution, role, 860

Page numbers in boldface refer to a major text discussion of the entry; page numbers with an F refer to a figure, with an FF to figures that follow consecutively; page numbers with a T refer to a table; vs means compare/comparison.

photosynthetic reaction centers, 827F, 850, 850F, 854F

Pus, 1531

Pyranosyl-RNA (p-RNA), 402F Pyrimidine base(s), 61, 116F

see also Cytosine; Thymine; Uracil Pyrophosphate release, DNA synthesis, 268F Pyruvate

anaerobic breakdown, 89–90, 90F citric acid cycle, 122F

glycolysis, 88, 89F, 121F oxidation to acetyl CoA, 96, 96F transport, 822

Pyruvate carboxylase, biotin use, 84F Pyruvate decarboxylase, 96F

Pyruvate dehydrogenase complex, 96, 96F Pyruvate kinase, 121F

Q

Q-cycle, 835–836

Quantitative reverse transcriptase polymerase chain reaction (RT-PCR), 573–574, 573F Quantum dots, 587, 588F Quaternary structure, 136 Quinone(s), 832F, 835, 851, 852F

R

Rab5, 762, 762F Rab effector(s), 761, 761F Rab GTPase(s), 760–761, 761, 761T Rabies virus, 1496F, 1517, 1518 receptor, 1505 Rac GTPase(s), 931

activation, microtubules role, 1043

effect on actin organization, 1042F, 1046–1047 epithelial apico-basal polarity, 1155F, 1156 growth cone steering, 1387

Rad51 protein, 307F see also RecA protein Rad52 protein, 308, 308F Radiation, DNA effects, 300–301

see also Ultraviolet (UV) radiation Radiofrequency, NMR, 529 Radioisotopes, 600–601, 601T

applications, 534, 602, 602–603, 602F, 603F see also Autoradiography

measurement, 601

Radiolabeling, 534, 602–603, 603F Radixin, 1009

Raf kinase (MAP-kinase-kinase-kinase), 929, 929F, 1239

RAG protein, 1563, 1564, 1564F, 1600 Ramachandran plot, peptide bond angles, 127F Random mutagenesis, gene expression analysis,

553, 556 Ran-GAP, 708 Ran-GEF, 708 Ran-GTP, 711 Ran GTPase(s) compartmentalization, 709F mitotic spindle formation, 1081 nuclear transport, 708–709, 709F, 710F Ran-GTPase-activating protein (Ran-GAP), 708 Ran-guanine exchange factor (Ran-GEF), 708 Ras gene, 1107, 1233–1234, 1241, 1242, 1242F Ras GTPase(s), 179, 180F, 926–927, 936F

activation of MAP-kinase pathway, 929F activation of PI 3-kinase, 934

active and inactive forms, 181F mitogen activation, 1103

mutated in cancers, 1107, 1233–1234, 1241 normal Ras proteins, 1234

as oncogene, 1107 regulation, GEFs, 927, 928F structure, 180F

Ras guanine nucleotide exchange factor (Ras GEF), 927, 928F

Ras–MAP-kinase signaling pathway, 928–930, 929F, 1103, 1176

Rb (retinoblastoma) gene/protein cancer, 1104–1105, 1234, 1235

cell cycle control, 1103–1105, 1104F, 1244F knock-out in mice, 1242

regulation by phosphorylation, 1104 ways of losing, 1236F

Reaction coupling, 75F, 78F, 824–825 activated carrier formation, 79–80 ATP role, 81

glycolysis, 91 mechanical model, 80F see also Free energy Reading frames

open see Open reading frames (ORFs) protein synthesis, 368, 368F RecA protein homologous recombination, 306–307, 307F synapsis, 307–308, 307F homologs, 307–308, 307F, 308F Brca1/Brac2 proteins, 310 protein–DNA interactions, 307F Receptor(s)

cell-surface see Cell-surface receptor(s) down-regulation, 795

editing, 1548, 1548F, 1565, 1565 see also Immunological tolerance intracellular, 881, 881F

see also Nuclear hormone receptor(s) ligand-gated ion channels see Ligand-gated ion

channel(s)

see also Receptor-mediated endocytosis; specific types

Receptor guanylyl cyclases, 922 Receptor-like tyrosine phosphatase, 922

see also Protein tyrosine phosphatases (PTPs) Receptor-mediated endocytosis, 784, 791–799

EGF uptake, 794

extracellular macromolecule import, 791–792, 793F

iron uptake, 794

material degradation, 793F membrane protein sorting, 794F receptor recycling, 792–794, 793F signal peptides, 792

transcytosis, 793F, 797–798, 797F Receptor proteins see Receptor(s)

Receptor serine kinase family, evolution, 177F Receptor tyrosine kinases (RTK), 922–924, 923F,

923T, 924FF, 925, 925F

In document NOTA SOBRE LAS ACCIONES (página 22-46)