Scheffler Immo E. Mitochondria

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INDEX 451

Membrane anchor proteins, 151

Membrane hyperpolarization, 240

Membrane potential, 31, 145

probing, 239–243

Menaquinone, 200

Mesohydrophobicity, 14

Messenger RNAs (mRNAs), 66, 67. See

also mRNA levels

differential turnover of, 124

partially edited, 123

peptides encoded by, 111

steady-state levels of, 89–90

turnover of, 90

Metabolic control analysis, 259, 265

applications of, 260

Metabolic diseases, 346

Metabolic disorders, 373

Metabolic network expansion, 10

Metabolic pathways

fatty acid metabolism and, 304–308

heme biosynthesis and, 309–314

iron–sulfur center biosynthesis and,

324–329

Krebs cycle and, 299–304

lipid biosynthesis/metabolism and,

314–318

in mitochondria, 298–344

small solute transport and, 329–340

ubiquinol biosynthesis and, 319–324

urea cycle and, 309

Metabolism, inborn errors of, 373

Metabolite transport, 334

Metal sites, complex IV, 214

Metazoan mtDNAs, noncoding region

in, 67

Metazoans

gene content and organization in,

mitochondrial genome in, 63–68

1-Methyl-4-phenylpyridinium (MPP

384

Methyl-malonyl-CoA mutase, 308

Mevalonate pathway, 319

mF plasmid, 79

(magnesium) ions, 336

MgADP, 252, 253

mgm1 mutant, 51

Mgm1p GTPase, 44

Mgm1p protein, 45

Microorganisms

mitochondrial mutations in, 348–350

studies of, xi

Microprojectile bombardment, 138

Microtubules, mitochondrial association

with, 34–36

Mif phenotypes, 53

Mild mutations, 361–362

Mitchell hypothesis, 228–236

mitK

ATP

channel, 336

Mitochondria

apoptosis and, 389–398

behavior and distribution of, 31

behavior during cell differentiation,

51–54

behavior when cells fuse, 45–46

biogenesis of, xii, 60–167

cell function and, 5–6

codon usage in, 126–128

distinguishing features of, 21–26

distribution during cell division,

46–51

distribution in the cytosol, 30–34

dynamic behavior of, xii

via electron microscope tomography,

evolutionary origin of, 7–17

functional characterization of, 299

importance of, xvi–xvii

import of transfer RNA into, 152–153

integration into the cell, 30–37

interaction with cytoskeleton, 34–37

interaction with intermediate

ﬁ laments, 37

lipid composition of, 314

metabolic pathways in, 298–344

monophyletic versus multiphyletic

origin of, 13

in multicellular organisms, 28–29

number per cell, 19–20, 96

oogenesis and, 362–366

outer and inner membranes of, 22

pharmacology and, 437–438

protein import into, 141–152

regulated protein degradation in,

153–156

relationship to bacteria, 8

reproducible isolation of, 169

RNA processing in, 113–116

452 INDEX

role in amino acid metabolism, 309

role in modern biology, xvi

shape and position of, 30

small solute transport and, 329–340

structure and morphology of, 18–30

structures identiﬁ ed as, 1–2

turnover and degradation of, 54

Mitochondrial biogenesis, control of,

Mitochondrial carrier protein family,

334–335

Mitochondrial defects, xv–xvi

Mitochondrial dehydrogenases, 338

Mitochondrial diseases, xiii–xiv, 5, 265,

345, 373

mtDNA mutations in, 354

nuclear mutations and, 373–377

Mitochondrial distribution and

morphology (MDM) genes, 47

Mitochondrial DNA (mtDNA), 4–5,

8–9, 11–12, 48–49. See also mtDNA

entries

aging and, 377–389

ampliﬁ cation of, 364

base changes in, 419

distribution in the zygote, 50–51

distributions in a pedigree, 356

in human–mouse interspecies cybrids,

in vitro system for initiating

transcription from, 107

linear, 63

molecular sizes of, 62

mutations in, 15

in oocytes, 357

Reclinomonas, 12

replication and maintenance of, 85,

96–105

Saccharomyces cerevisiae, 111, 226

sequence analysis of, 424

sequence variations in, 418

sequencing data derived from,

419–426

transcription in plant mitochondria,

111–113

uniparental transmission of, 354, 355

Mitochondrial DNA mutations,

346–347

clinical aspects of, 366–373

Mitochondrial DNA polymerase, strand

elongation by, 97

Mitochondrial DNA sequencing,

417–434

data derived from, 419–426

forensic applications of, 430–434

future challenges for, 434

Mitochondrial dysfunction, relationship

to Huntington’s disease, 388

Mitochondrial electron transfer,

168–297

chemiosmotic hypothesis and,

228–243

history of, 169–173

Mitochondrial encephalomyopathies

(MEM), 354, 355

maternal inheritance and, 359

Mitochondrial encephalomyopathy

with lactic acidosis and stroke-like

episodes (MELAS), 372. See also

MELAS (myopathy,

encephalopathy, lactic acidosis, and

stroke-like symptoms)

Mitochondrial enzymes, genes

encoding, 12

Mitochondrial Eve, 421, 422–423

Mitochondrial extracts, fractionations

of, 121

Mitochondrial factor, relationship to

prokaryotic factor, 135

Mitochondrial fusion assay, in vitro,

44–45

Mitochondrial fusion/ﬁ ssion, 37–46, 54

control of, 45

nucleod stability and, 110

Mitochondrial fusion-promoting (mF)

plasmid, 52, 53

Mitochondrial gene expression, 83

Mitochondrial (mt) genomes, 61–81, 123

arrangement of genes on, 69

co-evolution with nuclear genomes,

enzymes required for maintenance

and expression of, 82–85

in fungi, 72–75

genetic information in, 62–63

in kinetoplastid protozoa, 75–79

loss of, 14

in metazoans, 63–68

INDEX 453

number of, 63

in plants, 15, 68–72

size of, 68

Mitochondrial genotype, signiﬁ cant

change in, 362

Mitochondrial haplotypes, selective

advantage of, 434

Mitochondrial import stimulating factor

(MSF), 147–148

Mitochondrial inner membrane, yeast

translational activators and,

139–140

Mitochondrial intermediate peptidase

(MIP), 143

Mitochondrial iron homeostasis,

376

Mitochondrial matrix, 3

Mitochondrial medicine, 347

Mitochondrial membrane potential

maintaining, 274

probing with ﬂ uorescent dyes,

239–243

Mitochondrial morphology

dynamics of, 37–55

genes required for maintenance of,

49–50

manipulation and modulation of,

variation in, 29–30

Mitochondrial movements, dependence

on microtubules, 36

Mitochondrial mRNAs, translation of,

126–140

Mitochondrial mutations, 345–416

in cell culture, 348–354

in mammalian cells in culture,

350–354

in microorganisms, 348–350

myopathies caused by, 357

Mitochondrial NOS, 277

Mitochondrial nucleods, 52

Mitochondrial outer-membrane

permeabilization (MOMP),

394–395, 397

Mitochondrial oxidative damage,

reducing, 277

Mitochondrial peptidases, 143

Mitochondrial permeability transition

(MPT), 338–340

Mitochondrial permeability transition

pore, 338, 339

functions for, 340

Mitochondrial plasmids, 79–81

biological effects associated with,

80–81

Mitochondrial processing peptidase

(MPP), 205

Mitochondrial protein import, kinship

to active transport, 145

Mitochondrial proteins

identiﬁ cation of, 82, 142–143

nuclear genes encoding, 81–95

unfolded, 144

Mitochondrial protein synthesis, 134

mutant, 351

Mitochondrial proteome, 10

Mitochondrial respiration, 78

Mitochondrial (mt) ribosomes, 128–132

Mitochondrial shape changes, 37–46

Mitochondrial studies

history of, 1–6

inhibitors used in, 438

Mitochondrial topoisomerases, 82

Mitochondrial transcription factor

(mtTFA), 86, 103, 104, 108–109, 375

binding to D-loop DNA, 109

human and mouse, 109–110

Mitochondrial transcripts

polyadenylation of, 125

in yeast, 125

Mitochondrial transcriptional activator

(mtTFA), NRF-1 and, 92

“Mitochondriokinesis,” 41

Mitoﬁ lin, 26, 29

Mitofusin genes, 44

Mitophagy, 54

“Mitotic apparatus,” 9

Mitotic divisions, stability of

phenotypes during, 50

MMM genes, 47, 48, 49

mNOS, 278

Mohr–Tranebjaerg syndrome, 376–377

Molecular chaperones, 258

Molecular clock

calibration of, 421

estimated rates of, 420

Molecular genetics, of human

mitochondrial diseases, 354–377

454 INDEX

Monocistronic transcription, 112

Monoclonal antibodies, 146

Mouse embryos, manipulation of,

365–366

Mouse models, for Alzheimer’s disease,

386

MPP

analogues, inhibition mechanism

of, 193–195

MPTP (1-methyl-4-phenyl-1,2,3,6-

tetrahydropyridine), 193, 384

mRNA levels, control by turnover, 123–

125. See also Messenger RNAs

(mRNAs)

mtDNA4977 deletion, 388

mtDNA analysis, primate evolution

based on, 426–428. See also

Mitochondrial DNA entries

mtDNA damage

causes of, 381

normal aging and, 380–383

mtDNA deletions

age-related increase in, 380–381

gene loss and, 368

junctions and ﬂ anking regions of,

358–359

nondetectable, 359

mtDNA deletions/rearrangements, 355–

356, 367–369

mapping, 358–359

mtDNA depletion

familial, 369

syndromes resulting from, 375

mtDNA genealogical tree, 421

mtDNA haplotypes, variation in, 426

mtDNA maintenance/replication, 375

mtDNA molecules, 61–62

mtDNA mutations

accumulation of, 356–357

Alzheimer’s disease and, 387

mitochondrial diseases resulting

from, 361

mtDNA point mutations, 359–362

increase in, 379

mtDNA repair, in mammalian

mitochondria, 104–105

mtDNA replication, 366

check on, 102

in mammalian cells, 102–103

strand-asymmetric model of, 101

mtDNA replisome reconstitution, 97–98

mtDNA sequence data, 423

mTERF (mitochondrial transcription

termination factor), 113

Mtf1 protein, 111

mt-Hsp70 system, 154

mtRNA polymerase, 108

mtTFB1, methylating activity of, 108

mtTFB2, 108

Multicellular organisms, mitochondria

in, 28–29

Multicistronic transcription, 112

Multisite catalysis model, 251–252, 254

Muscle enhancer factor (MEF), 94–92

Mutant cell lines, isolating, 135–136

Mutants, screening for, 221

Mutated mtDNA, 368

Mutations. See also Mitochondrial

mutations; Nuclear mutations;

Point mutations

expressivity and penetrance of, 362

severe versus mild, 361–362

MWFE protein, 222

MWFE subunit, 192

Myoblast/myotube system, 94

Myoclonus epilepsy and ragged red

ﬁ bers (MERRF), 372

Myopathy and cardiomyopathy

(MIMyCa), 372. See also MELAS

(myopathy, encephalopathy, lactic

acidosis, and stroke-like symptoms)

NAD

(nicotinamide adenine

dinucleotide), 304

nad genes, 72, 73

NADH (reduced nicotinamide adenine

dinucleotide), accumulation of, 304

NADH dehydrogenases, 187, 227

NADH/NAD

ratio, 338

NADH oxidation, 226–227

in trypanosomes, 227–228

NADH supply, as a rate-limiting factor,

263

NADH-ubiquinone oxidoreductase,

185–195

NAD

/NADH, 329

NAD(P)H dehydrogenases, 224–225

antiport, 336. See also Proton

entries

INDEX 455

Nam1 protein, 140

nap cytoplasm, 400

ND6 peptide, 65

NDUFA1 gene, 222, 351

NDUFB11 gene, 351

NDUFS3-GFP expression system, 222

“Near equilibrium hypothesis,” 262

Nebenkern, 51

Neurites, mitochondrial movement in,

Neurodegenerative diseases, 383–389

Alzheimer’s disease, 386–387

amyotrophic lateral sclerosis, 389

Huntington’s disease, 387–389

Parkinson’s disease, 384–386

Neuronal NOS (nNOS), 277

Neuropathy, ataxia, retinitis pigmentosa

(NARP), 371–372

Neurospora, complex III in, 203

Neurospora crassa, 80, 141

complex I in, 186

complex III in, 202

studies using, 192

Neurospora intermedia, 80, 398

Nicholas II, Tsar, authentication of the

remains of, 431–432

NIF machinery, 325

Nigericin, 262, 329

Nitric oxide (NO), 277–279

actions on mitochondria, 278

as an inhibitor of cytochrome

oxidase, 278–279

long-term effect of, 279

properties of, 279

role in mitochondrial activity, xiii

Nitric oxide synthase (NOS), 277

NME1 gene, 105

nNOS, 277

Non-equilibrium thermodynamics

theory, 266

N-terminal, proteolytic processing of,

144

N-terminal targeting signals, 151

Nuclear DNA replication, 96–97

Nuclear gene products, 204

Nuclear genes, 83, 103

encoding mitochondrial proteins,

81–95

in eukaryotes, 258

Nuclear genomes, co-evolution with

mitochondrial genomes, 95

Nuclear-mitochondrial interactions, 404

Nuclear mutations, 136, 186, 346, 349

mitochondrial disease and, 373–377

Nuclear respiratory factor 1 (NRF-1),

Nuclear respiratory factor 2 (NRF-2),

92–93

Nuclear respiratory genes, regulation in

mammalian cells, 91–95

Nucleods, mtDNAs in, 110

Nucleo-mitochondrial interactions,

85–91

Nucleotide binding, 268

Nucleotide binding sites

noncatalytic, 252–253

“Nucleotide-induced recoupling,” 267

Nucleotides, conservation of, 129

Nucleotide transhydrogenase, 329–330

Null mutants, 47, 203–204

Null mutations, 186

nuo21 mutant, 192, 201

Nyctotherus ovalis, 15

NZB genotype, 365–366

OLE1 gene, 49

Oligomycin, 253–255, 261

Oligomycin sensitivity conferral protein

(OSCP), 244, 246, 249

subunit of, 253

ω genetic system, 73–74

Oocytes, mtDNA in, 357

Oogenesis, 96

mitochondria and, 362–366

OPA1 gene, 44

Open reading frames (ORFs), 66, 401,

402

identifying in plants, 121–122

in new mtDNA sequences, 65

in polycistronic transcripts, 132

in Saccharomyces cerevisiae, 73

Optical methods, 240

“Optional introns,” 73

orf224 chimeric gene, 401

orf239 peptide, 403

Osmotic reactions, versus chemiosmotic

reactions, 232

Outer membrane (OM) proteins, 148

456 INDEX

Oxa1 protein, 151

Oxidase activity, alternate, 225–226

Oxidases, in trypanosmatid

mitochondria, 228

Oxidative phosphorylation, 244

deﬁ ciencies in, 347

ﬂ uctuations in, 259

major reactions in, 261

Oxidative stress, 275, 276, 376, 379

Oxidized glutathione (GSSG), 275

OXPHOS capacity, 371, 372, 403

OXPHOS defects, 370, 373

OXPHOS deﬁ ciency, 374

OXPHOS dysfunction, 387

Oxygen

consumed during respiration, 171

partial reduction of, 218

reactions and, 274

Oxygen activation, 217–218

Oxygenic photosynthesis, evolution of,

p53 protein, 389

PAM complex, 149

“Pan-editing,” 121

Parkinsonism, pathways to, 386

Parkinson’s disease (PD), 384–386

PARK nuclear genes, 385

Paternal inheritance, 419

Pearson syndrome, 367–368

Pedigrees, genetic analysis of, 385

Penetrance, 362

Peptide compositions, comparison of,

188–189

Peptides

DNA sequences for, 65

in the F

core, 255

number manufactured, 106

Peptidyl transferase center (PTC), 129,

130

Permeability transition (PT), 393,

394

Peroxidases, 275

Peroxisomes, 299, 304

pet56 mutation, 129–130

PET111 gene, 136, 137

PET122 gene, 139

PET122 translational activator protein,

131

PET494 gene, 136, 137

PET494 mRNA, steady-state levels of,

140

Petite mutants, 83–84

from S. cerevisiae, 75

pet mutants, 204, 349

Pﬂ uger, E., 170

PGC-1 family coactivators, 93

Pharmacology, mitochondria and,

437–438

Phase contrast microscope, 30

pH gradient, 236

Phosphate transporter, 335

Phosphatidylcholine (PC), 318

Phosphatidylethanolamine (PE), 318

Phosphatidylglycerol (PG), 314, 315, 317

Phosphatidylserine synthase, 318

Phospholipids, biosynthesis of, 317

Phosphorylation, substrate-level versus

oxidative, 4

Photosynthetic reaction center (RC),

238

Phylogenetic Analysis Using Parsimony

(PAUP) program, 420

Phylogenetic trees, 175, 360, 420–423

Physarum polycephalum, 79, 117

mitochondrial fusions and genome

recombination in, 52–53

Phytopathogenicity, 81

Pichia pastoris, 28, 227

PIM1 gene, 153–154

pim1 mutants, 154

PIM1 protease, target of, 154

PINK1 kinase, 385

Plant mitochondria

editing in, 121–123

gene sequences of, 122

residual respiration by, 225

transcription of mtDNA in, 111–113

transcript processing in, 115

Plant mtDNAs, 71, 112

generalizations about, 68–70

Plants

cytoplasmic male sterility in,

400–404

mitochondrial genomes from, 62,

68–72

uncoupling in, 271–272

Plant tRNA genes, 152

INDEX 457

Plasmids

fungal senescence and, 398–399

as insertional mutagens, 80–81

mitochondrial, 79–81

Podospora anserina, 399

Point mutations, 349, 354, 369–373. See

also mtDNA point mutations

LHON-associated, 370

pol cytoplasm, 400, 401

Polyadenylation, 115

of mitochondrial transcripts, 125

Poly-(ADP ribose) polymerase (PARP),

392

Polycistronic RNA molecules, 66, 111

Polycistronic transcripts, 115

analysis of, 132

Polymerase chain reaction, 380

Polymerase γ family, 82

Polymerase γ genes, 97, 105

Polymorphisms, 104, 417. See also

Sequence heterogeneity

(polymorphisms)

human Y chromosome, 429

Polypeptides, 180

translocation of, 145

Polyprene tail, synthesis of, 319

polyQ peptide, 389

Potassium. See K

antiporter

P/O ratio, 234

Porin, 331

Porphyra purpurea, 11, 201

Post-translational protein import, 142

“Powerhouse of the cell,” 2

“Power stroke model,” 257

Prenyl transferase enzymes, 324

Presenilin-associated rhomboid-like

(PARL) protein, 45

Presenilin proteins, 386

Primary transcripts, 112

Primate evolution, 426–428

Primordial germ cells, 366

Programmed cell death, 389–390. See

also Apoptosis

Progressive external ophthalmoplegia

(PEO), 375

Prokaryotes

photosynthetic, 10

translation factors in, 133–134

Promoter elements, 91–95

Promoters

on mt genomes, 124

in plant mitochondria, 112–113

Propionyl-CoA, 308

Protease activity, 153–156

Proteases/peptidases, 83

Protein complexes, 179–182

complex I, 185–195

complex II, 195–202

complex III, 202–210

complex IV, 210–220

complex V, 244

Protein degradation, regulated,

153–156

Protein genes, cDNA clones for, 71

Protein import

machinery for, 145–152

into mitochondria, 141–152

system for, 141

Protein isoforms, encoded by gene

pairs, 88

Protein isoprenylation, 321–322

Protein-lipid ratio, in the inner

mitochondrial membrane, 29

Protein:nucleic acid ratio, in

mitochondrial ribosomes, 130

Protein/RNA interactions, mapping,

129

Proteins. See also Uncoupling proteins

in ﬁ ssion mechanism, 41–42

membrane insertion of, 151

mitochondrial targeting of, 141–145

release into cytosol, 394

required for mRNA translation, 110

Protein sequences, 127

Protein synthesis, mitochondrial, 13,

126

Proteomic studies, xii–xiii

Proto-eukaryote, 9

Proto-mitochondria, gene transfer from,

Protomitochondrial genes, 9

Proto-mitochondrion, 11

Proton electrochemical gradient, 236

Proton ﬂ ow, F

subcomplex and,

253–257

Proton gradient, 261–262, 266

Proton leakage, 235, 236, 265, 266, 329

Proton-translocating complex I, 228

458 INDEX

Proton translocation, 233–234, 235

D61 in, 256

ubiquinone in, 237

Proton transport/conductance, 269

“Proton wire,” 219

Protozoa, kinetoplastid, 75–79

PS decarboxylase, 318

Pseudogenes, 422

Pure mitochondria, isolating, 299

Purine nucleotides, 332

Pyruvate dehydrogenase, 303, 304

Pyruvate oxidation, 228

Q cycle, 207–209, 235, 237–239

center, 209

Quinone reduction center, 207

R210 residue, 256

Rab GTPases, 52

“Rapid replacement” model,

424–425

Reactive oxygen species (ROS), xiii, 5,

11, 218–219, 269, 270, 272–277

complexes implicated in, 273

damage caused by, 378–380

enzymes to guard against damage by,

274

increased production of, 275

major, 272–273

Reclinomonas americana, 201

mitochondrial genome of, 12

Recombinant reporter proteins,

Recombination, 358–359

illegitimate, 400, 402

Recombinational repair, 105

Recombination repeats, 69, 70, 400

in Arabidopsis thaliana mtDNA,

71–72

Redox couples, 184, 199

“Redox state,” xiii

REG1 gene, 89

Regulated protein degradation,

153–156

Regulatory molecules, 91

“Relaxed genomes,” 102

Renaturation kinetics, 76

Replica-plating techniques, 84

Respirasome, 183

Respiration

“glucose repression” of, 28

intracellular, 170

role of mitochondria in, 3

Respiration control, 259–272

major reactions in, 261

Respiration-deﬁ cient mutants, 349

“Respiration hot spots,” 243

“Respiratory pulse method,” 234–235

Respiratory enzyme, 171

Restorers of fertility (Rf), 81

Restriction analysis, 420

Restriction enzyme polymorphisms

(RFLPs), 53

Restriction mapping, 418

Reticulocyte lysate system, 142

Reticulomyxa, 36

Retrograde signaling process, 404

Retroposition mechanism, 121

“Reverse genetic approach,” 52

cells, 351, 382–383

Rhodamine 123 (Rh123) laser dye, 31,

240–243

Rhodamine staining, 19

Rhodobacter sphaeroidis, biophysical

studies on, 219–220

Rhodoquinone (RQ), 200, 324

Rho

−

mutants, 349, 352–352

Ribonucleoprotein complex, “active

sites” in, 129

Ribonucleoproteins, 100

Ribosomal peptides, 139

Ribosomal protein genes, 11–12, 70

Ribosomal proteins

classiﬁ cation of, 131

mutated, 139

Ribosomal RNA (rRNA), 12–13,

65, 82–83, 129. See also rRNA

entries

Ribosomes, mitochondrial, 128–132

Rieske iron–sulfur cluster, 205. See also

Iron– sulfur entries

Rieske iron–sulfur protein (ISP), 203,

237, 239

R-loop, 98, 99, 100, 101

Rml27p r-protein, 131

RNA (ribonucleic acid), endonucleolytic

processing of, 100

RNA–DNA hybrid, 100

INDEX 459

RNA editing

in vitro systems for, 123

in kinetoplastid protozoa, 116–121

in plant mitochondria, 121–123

in trypanosomes, 119–120

RNA polymerases, in plants, 113

RNA processing, in mitochondria,

113–116

RNase MRP (mitochondrial RNA

processing), 100–101

RNase MRP gene, 105

RNase P, 114–115

Rockefeller Institute, 20

Rotary motors, types of, 250–251

“Rotating” three-site model, 250

Rotenone, 193, 276, 384

Rotenone-insensitive dehydrogenase,

225

Rotenone-resistant enzymes, 227

ROX1 gene, 88–89

R-plasmids, 81

rRNA comparisons, phylogenetic trees

based on, 13. See also Ribosomal

RNA (rRNA)

rRNA sequence comparisons, 13

Saccharomyces cerevisiae, xvii, 9, 72–75,

absence of complex I in, 226–227

cell division in, 46

mitochondrial morphology in, 28

as a model system, 348

mtDNA transcription in, 111

mutants of, 135, 136

PET genes of, 84

petite mutants from, 75

reticular structures in, 38

uncoupling in, 271

Salicylic acid, 226

“Sampling and ampliﬁ cation”

mechanism, 362–363

Sauromatum guttatum, 225

Schistosoma mansoni, 200

Schizosaccharomyces pombe, 72, 225

SDH1 gene, 196

SDH2 promoter, 94

SDH activity, mammalian cell mutant

defective in, 201–202

SDHB gene, 11

SDHB subunit, 326–327

SDHC gene, 11

SDH complex, 197

Semiquinone, 237

senDNAs, 399

Senescence, fungal, 80–81

Sensorineural hearing loss, 372–373

Sequence blocks, 129

Sequence conservation, 107, 253

Sequence divergence, in plants, 70

Sequence heterogeneity

(polymorphisms), 104. See also

Polymorphisms

from human population groups,

425–426

Serial Endosymbiotic Theory,

8–9

Severe mutations, 361–362

SfaNI mutation, 360

Shine–Dalgarno sequence, 134

Single nucleotide polymorphism (SNP),

359

Single-point mutations, 360–361

Skeletal muscle, mitochondria in, 33

“Slipping pump,” 265

“Slip-replication,” 381

Slow dyes, 243

Small solute transport, 329–340

“Small Tims,” 148–149, 150

s mutants, complex III, 204

SNARE complex, 52

Snf1 kinase, 89, 90

S-nitrosoacetyl penicillamine (SNAP),

279

SOD1 gene, 389

Sodium. See F-type Na

-ATPase rotor

ring; Na

antiport

Sorting and assembly machinery (SAM)

complex, 148

Spacer DNA, 72

Spectroscopic techniques, 177

S-plasmids, 81

Sporadic inheritance, versus maternal

inheritance, 355–357

s-rRNAs, 129

SRY gene, 429

Staining methods, 19

Steroid secreting cells, 28

Stop-transfer signal, 150

460 INDEX

Strand-asymmetric model, of mtDNA

replication, 101

Strand-displacement model, 101

Structural genes, variations in, 67–68

Structure–function studies, 256

Subcellular membranous structures,

fractionation of, 318

“Subgenomic pathway,” 75

“Sublimons,” 70

Substrate dehydrogenation, 266

“Substrate-level phosphorylation,” 173

Substrate oxidation, 265, 266

Substrate protons, 235

Substrates, role in respiration control,

261–266

Subunits

of ATP synthase, 246–247

complex III, 202–204

complex IV, 212–213

Succinate dehydrogenase (SDH), 11,

177, 300, 303

Succinate:ubiquinone oxidoreductase,

195–202

Succinyl-CoA, 300, 310

Succinyl-CoA synthetase, 303

SUF machinery, 325

Sunﬂ ower, male sterility in, 402–403

Supercomplexes, 182–184

formation of, 183–184

“Supernumerary” subunits, 186, 222,

223

Superoxide anions, 276–277

Superoxide dismutase (SOD), 274–275

Superoxide formation, 275–276

Superoxide radical, 272, 273, 274

SURF-1 gene product, 224

SURF-1/Shy1 gene, 223

“Symmetry mismatch,” 257

“Synaptic” regions, 338

α-Synuclein, 385

Systems biology, xiv

Tafazzin, 280–281, 317

Targeting sequences, 143

TAZ gene, 280, 317

Temperature sensitive mutants,

145

Terminal inverted repeat (TIR)

sequences, 53, 79

Termination-associated sequences

(TASs), 101–102

Termination codons, 126

Termination factors (TFs), 133

Ternary complexes, 334

TFAM (transcription factor A

mitochondrial), 103–104

Thermodynamics, 169–170

Thermogenesis, 266–267

Thermogenic capacity, 268

Thermogenin, 267. See also UCP-1

(thermogenin)

uncoupling by, 268

Thermoregulation, 267

Thermus thermophilus, subcomplex

structure in, 190–191

Thiokinases, 305

3-D imaging, 26

3′UTRs, 132

Thunberg, T., 172

TIM22, 150

TIM23, 149–150, 151

TIM complex, 144, 146, 147, 149. See

also “Small Tims”

“Time to the most recent ancestor”

(TMRCA), 423

TIMM genes, 377

Tissue culture, investigating DNA

replication in, 96–104

TOM complex, 144, 146, 147, 148

“Topiary pruning” method, 420

Transcription, 140

in mammalian mitochondria, 105–110

mechanism and machinery of, 110

termination of, 113

Transcription factors, 279

Transcription initiation sites, 111

Transcripts, partially edited, 123

Transfer RNAs (tRNAs), 62, 66, 71,

107. See also tRNA entries

import of, 152–153

processing of, 115

sequencing of, 127–128

splicing out, 114–115

Translation, of mitochondrial mRNAs,

126–140

Translational activators

membrane-associated, 139–140

properties of, 139–140