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Note: Page numbers followed by f indicate figures; those followed by t indicate tables.

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A site, 298, 298f, 299, 300f

ABO blood group antigens, 92–93, 92f, 95

Bombay phenotype and, 95

Acentric chromatids, 158

Acetylation, histone, in gene regulation, 323–324

Acquired immunodeficiency syndrome, 199–200

Acquired traits, inheritance of, 47

Acridine orange, as mutagen, 359, 359f

Acrocentric chromosomes, 22, 22f, 150

Addition rule, 52–54, 53f

Additive genetic variance, 455

Adenine, 214–215, 215f, 216–217, 216t, 217f. See also Base(s)

Adenomatous polyps, colon cancer and, 437–438, 437f

Adenosine monophosphate (AMP)

in catabolite repression, 320

in translation, 296

Adenosine triphosphate (ATP), in translation, 296

Adenosine-3′, 5′ cyclic monophosphate (cAMP), in catabolite repression, 320

A-DNA, 218, 218f

Agar plates, 179, 179f, 180f

Age, maternal, aneuploidy and, 164–165

Aging

premature, 249–250

telomere shortening and, 249–250

Agriculture. See also Breeding; Crop plants

genetics in, 3, 3f, 7–8, 7f

in genetic engineering, 395

quantitative, 445–446

Agrobacterium tumefaciens, in cloning, 379

AIDS, 199–200

Alanine, 291t

Albinism. See also Color/pigmentation

in Hopi, 1–2, 2f

Alkylating agents, as mutagens, 357

Alleles, 11, 21. See also Gene(s)

in crossing-over, 27, 28f

definition of, 46, 46t

dominant, 48, 49f, 89

lethal, 91–92

molecular nature of, 51

multiple, 92–93, 92f

notation for, 48–50, 54–55

paramutation and, 335, 335f

recessive, 48

segregation of, 48, 51f, 56f, 58–60, 116–117

temperature-sensitive, 103

wild-type, 54

Allelic fixation, 480

Allelic frequencies

calculation of, 471–472

at equilibrium, 477

estimation of, 476

fixation and, 480

genetic drift and, 479f, 480, 482–483, 482t

Hardy-Weinberg law and, 476

migration and, 477–478, 478f, 482–483, 482t

for multiple alleles, 471–472

mutation and, 476–477, 477f, 482–483, 482t

natural selection and, 480–483, 481t, 482t, 483f

nonrandom mating and, 476

for X-linked alleles, 471

Allelic series, 92–93

Allolactose, 314, 315, 315f

Allopatric speciation, 485–487, 485f

Allopolyploidy, 166, 167–168, 168f, 169t

Allosteric proteins, 311

Alpha helix, 218, 218f, 291, 292f

Alternation of generations, 35, 35f

Alternative processing/splicing, 276f

in gene regulation, 327–328, 328f

of mRNA, 276, 276f

Alu elements, 363

Amanitin, 259–260

American Indians, albinism in, 1–2, 2f

Ames test, 360, 360f

Amino acids, 290–291

assembly into proteins, 295–301. See also Translation

in genetic code, 291–295, 293f, 294f

peptide bonds of, 290, 292f, 298, 299f

sequence of, 291–295, 292f

structure of, 290–291, 291f

triplet code and, 292

types of, 291t, 293f

Aminoacyl (A) site, 298, 298f, 299, 300f

Aminoacyl-tRNA

synthesis of, 296

in translation, 329–330

Aminoacyl-tRNA synthetases, 296

AMP (adenosine monophosphate)

cyclic, in catabolite repression, 320

in translation, 296

Amphidiploid, 168

Anagenesis, 483

Anaphase

in meiosis, 28, 28f, 30t

in mitosis, 24f, 25, 25t, 29

Anemia, Fanconi, 365t

Aneuploidy, 151, 151f, 161–165, 169t

autosomal, 163, 165f

cancer and, 165

causes of, 161, 162f

definition of, 161

in Down syndrome, 163–164, 163f–165f

in Edward syndrome, 164

in humans, 163–165

maternal age and, 164–165, 165f

in Patau syndrome, 164

phenotypic effects of, 162

rate of, 163

of sex chromosomes, 162

in Klinefelter syndrome, 80, 87

in Turner syndrome, 80, 87

in trisomy 8, 164

types of, 161–162

Angiosperms. See also Arabidopsis thaliana (thale cress); Plants

cytoplasmic inheritance in, 100

flower color in

inheritance of, 89, 89f

lethal alleles and, 91

flower length in, inheritance of, 453–454, 453f

Animals

breeding of, 7–8, 94, 395

artificial selection in, 459–460

quantitative genetics in, 445–446

coat color in. See Coat color

maternal behavior in, epigenetics and, 335–336

sexual reproduction in, 34–35, 34f

transgenic, 391–392, 391f, 395

Anopheles gambiae (mosquito), genome of, 416, 416t

Antibiotics

resistance to, gene transfer and, 189

translation and, 302–303

Anticodons, 278, 278f

Antigenic drift, 201

Antigenic shift, 201

Antigens, blood group, 92–93, 92f

ABO, 92–93, 92f, 95

Bombay phenotype and, 95

MN, 89

Antiparallel DNA strands, 216, 217f

APC gene, in colon cancer, 437f, 438, 439

Apoptosis, 435

Arabidopsis thaliana (thale cress)

gene regulation in, 324

genetic techniques with, 332, 332f, 333

genome of, 332, 332f, 416, 416t, 417t

histone acetylation in, 324

life cycle of, 332f, 333

as model genetic organism, 5, 331–333

translation in, inhibition of, 329

Archaea, 19. See also Bacteria; Prokaryotes

genome of, 414, 415t

replication in, 250

Arginine, 291t

Artificial chromosomes

in genome sequencing, 406–407

as vectors, 379

Artificial selection, 459–460. See also Breeding

Asexual reproduction, polyploidy and, 169

Asparagine, 291t

Aspartate, 291t

Assortive mating, in sympatric speciation, 488

Astbury, William, 213

ATP (adenosine triphosphate), in translation, 296

Autopolyploidy, 166–167, 166f, 169t

Autosomal aneuploidy, 163, 163f, 164f, 165f

Autosomal traits

definition of, 63

dominant, 63, 65

recessive, 64f, 65

Autosomes, 77. See also Sex chromosomes

Auxotrophs, 179, 179f

Avery, Oswald, 210–211

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Bacillus thuringiensis, 395

Backcross, 51

Bacteria. See also Escherichia coli (bacterium)

antibiotic resistance in, 189

archaea, 19. See also Archaea

auxotrophic, 179, 179f

cell reproduction in, 20. See also Replication

cell structure in, 18f, 19

conjugation in, 182–189, 183f–188f, 187t, 316–317. See also Conjugation

culture of, 179f, 191

diversity of, 178–179

DNA in, 19, 19f, 181, 181f, 220f, 221, 221f

eubacteria, 19. See also Eubacteria

gene mapping in, 190f, 194–196, 197f

gene regulation in, 307–322

vs. in eukaryotes, 322, 330–331

gene transfer in, 182–192

by conjugation, 182–189, 183f–188f

horizontal, 191, 494

by transduction, 182, 183f, 194–195, 195f, 196f

by transformation, 182, 183f, 189–190, 190f

genes of, 19–20, 191, 192f

function of, 415f

number of, 414, 415t

in genetic studies, 178t

genetically modified, industrial uses of, 395

gut, obesity and, 411

mutant strains of, 179, 179f

number of, 177–178

operons in, 307–308. See also lac operon

overview of, 177–178

phages and, 193–198. See also Bacteriophage(s)

prokaryotic, 11. See also Prokaryotes

prototrophic, 179

recombination in, 250–251

replication in, 235–238, 237f, 240–246

transcription in, 266–270

transduction in, 182, 183f, 194–195, 195f, 196f. See also Transduction

transformation in, 182, 183f, 189–190, 189f, 190f

in cloning, 377

in gene mapping, 189–190, 190f

translation in, 295–301

wild-type, 179

Bacterial artificial chromosomes (BACs)

in genome sequencing, 406–407

as vectors, 379

Bacterial chromosomes, 19, 19f, 180–181, 181f, 187, 190f, 191, 192f

DNA packaging in, 220f, 221, 221f

Bacterial colonies, 179–180, 179f, 191

Bacterial cultures, 179f, 191

Bacterial genome, 18f, 19,180–181, 181f, 191, 192f

sequencing of, 414, 415t

Bacterial plasmids. See Plasmid(s)

Bacteriophage(s), 193–198, 379, 379t

in bacterial gene mapping, 197f

culture of, 192, 192f

DNA in, 211–212, 211f, 212f

experimental advantages of, 191–192

experimental techniques with, 194

gene mapping in, 197–198

in Hershey-Chase experiment, 211–212, 211f

lambda, 379, 379t

life cycle of, 192f, 193

prophage, 193, 193f

reproduction of, 211–212, 211f

T2, 211–212, 211f

temperate, 193, 193f

transducing, 194–195

virulent, 193, 193f

Baldness, 115–116

Bananas, 149–150

Banding, chromosome, 150–151

Bar mutations, 152–153, 153f

Barr, Murray, 86

Barr bodies, 86, 86f, 87t

Barry, Joan, 93

Basal transcription apparatus, 325–326

Base(s), 209, 209t, 214–215, 215f, 216t, 217f, 218f. See also Nucleotide(s) and specific bases

Chargraff’s rules for, 209, 209t

methylation of, 325. See also DNA methylation

modified, 278

purine, 214, 215f

pyrimidine, 214, 215f

ratios of, 209, 209t

RNA, 260–261, 261t

sequence of, 219

in Watson-Crick model, 213–214, 215f

Base analogs, as mutagens, 356–357, 357f

Base pairing

in codons, 292, 294f

deamination and

induced, 358, 358f

spontaneous, 356–357, 356f, 357f

depurination and, 356, 356f

in double helix, 216–217, 217f

mutations and, 354f, 355

Ames test and, 360, 360f

nonstandard, 354f, 355

tautomeric shifts in, 354f, 355

in translation of genetic code, 292, 294f

wobble in, 294, 294f, 354f, 355, 355f

Base substitution mutations, 347–350, 347f, 350f, 352f

Base-excision repair, 364–365

Bateson, William, 117

Baur, Erwin, 91

B-DNA, 218, 218f

Beadle, George, 290

Beadle-Tatum one gene, one enzyme hypothesis, 290

Bees, genome of, 403–404

Benzer’s mapping technique, 198

Beta pleated sheet, 291, 292f

Bidirectional replication, 237–238

Binary fission, 20

Biodiversity, genetic engineering and, 395

Bioinformatics, 410

Biological evolution, 483. See also Evolution

Biological species concept, 484

Biology

genetics in, 4

synthetic, 411–412

Biotechnology, 3, 372, 394–396. See also Recombinant DNA technology

Bishop, Michael, 432

Bivalent, 27

Blending inheritance, 8

Blind men’s riddle, 17–18

Blindness

in Leber congenital amaurosis, 371–372

in Leber hereditary optic neuropathy, 101

Blood group antigens, 92–93, 92f

ABO, 92–93, 92f, 95

Bombay phenotype and, 95

MN, 89

Bodmer, Rolf, 345

Bonds

hydrogen, in DNA, 216–217, 217f

peptide, 290, 292f, 298, 299f

phosphodiester, 215, 217f

Boundary elements, 326–327, 327f

Boveri, Theodor, 50

Bowen-Conradi syndrome, 289–290

Boycott, A., 75–76

Bradyrhizobium japonicum, genome of, 414, 415t

Branch diagrams, 57–58, 58f, 59f

Branch point, 275

Branches, of phylogenetic trees, 489, 489f

Bread mold (Neurospora crassa), 5

Breast cancer

BRCA1/BRCA2 genes in, 431, 432t, 434

progression of, microarrays and, 412–413

Breeding

of animals, 7–8, 94, 391–392, 391f, 395

artificial selection and, 459–460

of plants, 3, 3f, 7–8, 7f, 167–168, 168f

quantitative genetics in, 445–446

Bridges, Calvin, 79–80

Broad-sense heritability, 455

5-Bromouracil, as mutagen, 357, 357f

Broth, 179

Bt toxin, 395

Bulbar muscular atrophy, 348t

Burkitt lymphoma, 439, 439f, 440

Bush, Guy, 488

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C banding, 151, 151f

Caenorhabditis elegans (nematode)

genome of, 281–282, 282f, 416, 416t, 417t

life cycle of, 281

as model genetic organism, 5, 6f, 281–283, 282f, 283f

transgenic, 283, 283f

cAMP, in catabolite repression, 320

Camptothecin, 233–234

Cancer

abnormal cell growth in, 434–435

aneuploidy and, 165

angiogenesis in, 436

apoptosis and, 435

breast, 412–413, 431, 434, 434t

Burkitt lymphoma, 439, 439f, 440

cervical, 414, 440

chemotherapy for, 233–234

chromosome abnormalities in, 434, 438–439, 439f

clonal evolution of, 430–431, 431f

colorectal, 365, 365t, 437–438, 437f, 439

DNA methylation in, 437

DNA repair in, 365, 365t, 435–436

environmental factors in, 431–432, 431t, 432t

epigenetic changes in, 436–437

follicular lymphoma, 436–437

as genetic disease, 429–431

genomic instability in, 439

haploinsufficiency and, 434

incidence of, 429t

Knudson’s multistep hypothesis for, 429–430, 430f

loss of heterozygosity in, 432–433, 434f

lung, 432

metastasis in, 429, 436

microRNA in, 413–414

mutations in, 360, 360f, 429–431, 434–439, 439f

oncogenes in, 432–433, 433f

pancreatic, 427–428, 428f

progression of, microarrays and, 412–414

retinoblastoma, 429–430, 430f, 434

retroviruses and, 199

skin, in xeroderma pigmentosum, 365, 365f, 365t, 430–431, 436

stimulatory genes in, 432

telomerase in, 250, 436

topoisomerases and, 233–234

tumor-suppressor genes in, 432, 433–434, 433f, 434t

two-hit hypothesis for, 429–430, 430f

viruses and, 440–441, 440f

in von Hippel-Lindau disease, 436

Capsicum annuum (pepper), fruit color in, 92f, 93–94

Carcinogens

Ames test for, 360, 360f

environmental, 431–432

Carriers, translocation, 164, 165f

Catabolite activator protein, 320

Catabolite repression, 320

Cats, coat color in, 87, 87f

Cavalli-Sforza, Luca, 480

Cavenne, Webster, 434

cDNA libraries, 381–382

Cech, Thomas, 260

Cell(s)

competent, 189

diploid, 21, 21f

eukaryotic, 11, 18f, 19–20. See also Eukaryotes

genetic material in, 18f, 19–20, 19f

haploid, 21

information pathways in, 218f, 219

prokaryotic, 11, 18f, 19–20. See also Prokaryotes

reproduction of, 20–26

structure of, 18f, 19

transformant, 190

Cell cycle, 22–26. See also Meiosis; Mitosis

in cancer, 434–435

centromeres in, 225

checkpoints in, 22–23, 23f, 25, 435f

chromosome movement in, 23–25, 24f

chromosome number in, 26, 26f

definition of, 22

DNA molecule number in, 26, 26f

DNA synthesis in, 23, 25–26

genetic consequences of, 25–26

interphase in, 22–23, 23f, 24f, 25t

overview of, 23f, 25t

phases of, 23–25

G₀, 23, 23f, 25t

G₁, 23, 23f, 25t

G₂, 23, 23f, 25t

M, 23–25, 23f, 24f, 25t, 26

S, 23, 23f, 25t, 26

regulation of, 434–435

replication in, 23–25, 23f, 25t. See also Replication

Cell division

in cytokinesis, 23, 23f

cytoplasmic, 23, 23f

in eukaryotes, 20–26. See also Cell cycle

in meiosis, 27–37

in mitosis, 23–25, 23f, 25t, 32, 32f

in prokaryotes, 19f, 20

Cell growth, in cancer, 428–429, 434–435

Cell theory, 9, 9t

CenH3 histone, 225

CentiMorgan (cM), 127

Central dogma, 219, 260

Centrifugation, equilibrium density gradient, 235–236, 235f

Centrioles, 25

Centromeres, 21–22, 22f, 225

in chromosome movement, 225

counting of, 26

definition of, 225

structure of, 225

Centrosomes, 24f, 25

Cerebellar ataxia, 348t

Cervical cancer, 414, 440

CFTR mutations, in cystic fibrosis, 90

Chaperones, 302

Chaplin, Charlie, 93

Characteristics

continuous (quantitative), 104, 445–462. See also Quantitative characteristics

definition of, 46t

discontinuous (qualitative), 104, 446–447, 446f

homologous, 488–490

meristic, 448

multifactorial, 104

sex-limited, 99, 100r, 102t

sex-linked, 81–88, 102t. See also Sex-linked characteristics

threshold, 448

vs. traits, 46. See also Traits

Chargraff, Erwin, 209, 213

Chargraff’s rules, 209, 209t

Chase, Martha, 211–212

Checkpoints, in cell cycle, 22–23, 23f, 25, 435f

Chemical mutagens, 357–359

Cheng, Keith, 6

Chiasma, 27

Chickens, feathering patterns in, 99

Chimpanzees, chromosomes in, 156, 156f

Chi-square distribution, critical values for, 62t

Chi-square goodness-of-fit test, 61–62

for crosses/linkages, 61–62, 62t, 63f, 126f

for Hardy-Weinberg proportions, 475

for independent assortment, 125, 126–127

Chi-square test of independence, 125, 126–127, 126f

Chloroplast DNA (cpDNA), 100, 227

Chromatids

acentric, 158

dicentric, 158

nonsister, in crossing over, 28f, 29–32

sister, 22, 22f

counting of, 26

separation of, 23–25, 24f, 25t, 28

Chromatin, 19, 19f, 222–224, 223f, 224f

epigenetics and, 224

nucleosome in, 222–223, 224f

proteins in, 222–223, 223f

structure of, 19, 19f, 222–224, 223f, 224f

changes in, 224, 322–325, 336

gene expression and, 224, 323

levels of, 222–223, 223f

types of, 222

Chromatin-remodeling complexes, 323

Chromosomal proteins, nonhistone, 222

Chromosome(s)

acrocentric, 22, 22f, 150

bacterial, 19, 19f, 180–181, 181f, 187, 190f, 191, 192f

DNA packaging in, 220f, 221, 221f

bacterial artificial

in genome sequencing, 406–407

as vectors, 379

in chimpanzees vs. humans, 156, 156f

chromatin in. See Chromatin

condensation of, 24f, 27, 28f

counting of, 26, 26f

coupling configurations for, 122, 123f

crossing over of. See Crossing over

daughter, formation of, 24f, 25, 26

in diploid organisms, 21, 22f

DNA packaging in, 21, 220–224

in bacterial chromosome, 221, 221f

in eukaryotic chromosome, 221–224, 221f, 223f–225f

ends of, 22, 22f, 24f, 225

replication at, 225, 248–250, 248f, 249f

sticky (cohesive), 22, 22f

eukaryotic, 19, 19f, 21–22

DNA packaging in, 220–225, 220f

fragile sites on, 160–161, 160f

gene density in, 226, 227, 418

gene location on, 12, 12f. See also Gene loci

in haploid organisms, 21

homologous pairs of, 21, 21f, 29–32

separation of, 31, 31f, 33–34, 33f, 50–51

karyotypes and. See Karyotypes

mapping of. See Gene mapping

in meiosis, 27–37, 49f, 50–51

metacentric, 22, 22f, 150

in mitosis, 23–25, 24f, 25t

morphology of, 150, 151f

movement of, 24f, 25

centromeres in, 225

nondisjunction of. See Nondisjunction

nonsex, 77

number of, 21, 21f

abnormal, 161–165. See also Aneuploidy; Polyploidy

origins of replication of, 20, 22

Philadelphia, 438–439

prokaryotic, 19, 19f

proteins in, 222–224. See also Chromatin;

histone, 222–223

nonhistone, 222

random distribution of, 31, 31f

replication of, 20, 22, 22f, 24f. See also Cell cycle

in repulsion, 122, 123f

segregation of. See Segregation

sets of, 21, 21f

sex. See Sex chromosomes

shortening of, 225

staining of, 150–151, 151f

structure of, 21–22, 22f, 150–151, 151f, 221–224

submetacentric, 22, 22f, 150

synapsis of, 27

telocentric, 22, 22f, 150

telomeric sequences in, 22, 22f, 225, 225f

yeast artificial, in genome sequencing, 406–407

Chromosome banding, 150–151, 151f

Chromosome mutations, 150. See also Mutation(s)

aneuploid, 161–165

in evolution, 170

polyploid, 166–170

rearrangements, 152–161

types of, 151

Chromosome rearrangements, 152–161, 155t, 170t. See also Mutation(s)

copy-number variations, 161

deletions, 155–156, 155f, 155t, 156f, 170t, 347f, 348, 353t, 355–356, 356f

duplications, 151f–153f, 152–154, 155t, 170t, 494. See also Duplications

in evolution, 170

inversions, 156–159, 156f–159f, 170t

in cancer, 438–439

phenotypic consequences of, 152–153, 153f, 154f, 155t

translocations, 159–160, 170t. See also Translocation(s)

Chromosome theory of heredity, 50–51, 117

Chromosome variation, 149–171, 170t. See also Mutation(s)

Chronic myelogenous leukemia, 438–439, 439f

Circular chromosome, bacterial, 180–181, 181f

Circular DNA

bacterial, 181, 181f

replication in, 248–249

Cis configuration, 122, 123f

Cladogenesis, 483–484

Clawed frog (Xenopus laevis), 5

Cleavage, in RNA processing, 251, 274, 275f, 329

Clonal evolution, 430–431, 431f

Cloning, 377–379

definition of, 377

DNA libraries for, 381–382

positional, 382–383

restriction, 377–379

selectable markers in, 377–379, 378f

transformation in, 377

vs. polymerase chain reaction, 380

Cloning vectors, 377–379

bacterial artificial chromosome, 379

bacteriophage, 379, 379f

cosmid, 379, 379t

definition of, 377

for eukaryotes, 379

expression, 379, 379f

in gene therapy, 396

plasmid, 377–379, 378f, 379f, 379t

replacement, 379

selectable markers for, 377–379

Ti plasmid, 379

Closed loop, 297, 299f

Cloverleaf structure, 278, 278f

c-MYC gene, in Burkitt lymphoma, 439

Coactivators, 325–326

Coat color

in cats, 87, 87f

lethal alleles and, 91

in mice, 91

in rabbits, 103, 103f

Cock feathering, 99

Cockayne syndrome, 365t

CODIS, 390, 390t

Codominance, 89–90, 90t

Codons, 273, 273f

base pairing in, 292, 294f

in genetic code, 292–295, 294f

nonsense, 295

reading frames and, 295, 348

sense, 293

start (initiation), 273, 295

stop (termination), 273, 295, 299, 300f

synonymous, 293

Coefficient of coincidence, 134–135

Cohesin, 33–34, 33f

Cohesive (sticky) ends

of chromosomes, 22, 22f

of DNA fragments, 374, 374f

Colchicine, 166

Colinearity, of genes and proteins, 271–272

Collins, Francis, 408f

Colon cancer, 439

faulty DNA repair in, 365, 365t

mutations in, 437–438, 437f

Colonies, bacterial, 179–180, 179f

Color blindness, 84–85, 85f

Color/pigmentation

body

in D. melanogaster, 82f, 98, 129–135, 131f, 133f, 134f, 492–493, 493f

as X-linked characteristic, 81–82, 82f

evolution of, 492–493, 493f

flower

inheritance of, 89, 89f

lethal alleles and, 91

fruit

epistasis and, 95–96, 96f

gene interaction and, 93–94, 96f

gene interaction and, 93–98, 96f

hair, 43–44. See also Coat color

inheritance of, 43–44, 448–450, 450f

leaf, cytoplasmic inheritance and, 100, 100f

temperature-dependent, 103, 103f

wheat kernel, 448–450, 450f

Combined DNA Index System (CODIS), 390, 390t

Comparative genomics, 414–419

eukaryotic genomes and, 415–419

prokaryotic genomes and, 414–415

Competence, cellular, 189

Complementary DNA strands, 216–217

Complementation, 98

Complementation tests, 98

Complete dominance, 89, 89f, 90t

Complete linkage, 119f, 120f, 123–124

vs. independent assortment, 118–120

Complete medium, 179

Compound heterozygotes, 93

Conditional mutations, 350

Conditional probability, 54

Congenital heart disease, 345

Conjugation, 182–189, 183f–188f, 187t

in Davis’ U-tube experiment, 184, 185f

F′ cells in, 186–187, 187t

F⁺ cells in, 184–185, 185f–187f, 187t

F⁻ cells in, 184–185, 185f–187f, 187, 187t

F factor in, 181, 181f, 184–187, 185f–187f, 187t

Hfr cells in, 185–186, 187t

interrupted, in gene mapping, 187

in Lederberg-Tatum experiment, 182–184

Consanguinity, 64, 65f

Consensus sequences

in bacteria, 267–268, 267f

poly(A). See Poly(A) tail

Shine-Dalgarno, 273, 273f, 297, 297f, 301

in splicing, 275–276, 275f

Conservative replication, 234–235, 235f. See also Replication

Constitutive mutations, 317

Contigs, 406

Continuous characteristics. See Quantitative characteristics

Continuous replication, 240, 240f

Coordinate induction, 315

Copy-number variations, 161

Core enzyme, 266

Corepressors, 312

Corn (Zea mays), 5

Correns, Carl, 45, 100

Cosmid vectors, 379, 379t

Cotransduction, 194

Cotransformation, 190, 190f

Coupling (cis) configuration, 122–124, 123f

cpDNA (chloroplast DNA), 100

C-rich strand, of telomere, 225, 225f

Crick, Francis, 10, 208, 213–214, 213f, 219, 271, 291, 294

Cri-du-chat syndrome, 155t

CRISPR RNA (crRNA), 262, 262t. See also RNA

Crop plants. See also Plants

breeding of, 3, 3f, 7–8, 7f, 167–168, 168f

genetically modified, 3, 3f, 395

herbicide-resistant, 395

Crosses, 29–32, 30f–32f, 30t, 32f

addition rule for, 52–54, 53f

backcrosses, 51

bacteriophage, 197–198

branch diagrams for, 57–58, 58f, 59f

chi-square goodness-of-fit test for, 61–62, 62t, 63f, 125–127, 126f

cis configuration in, 122, 123f

dihybrid, 55–60, 56f, 58f, 59f

genotypic ratios in, 55, 55t

with linked genes, 117–127. See also Linkage

coupling in, 122, 123f

notation for, 118

predicting outcome of, 124–125

recombination frequency for, 121

in repulsion, 122, 123f

testcrosses for, 118–120, 119f

meiosis and, 50–51

monohybrid, 47–55

multiple-loci, 55–60

multiplication rule for, 52, 53–54, 53f

Nilsson-Ehle’s, 448–450

notation for, 48–50, 54–55, 118

outcome prediction for, 51–54, 124–125

phenotypic ratios for, 54–55, 55t

observed vs. expected, 60–62, 63f

probability rules for, 52–53, 53f, 57–58, 58f, 59f

Punnett square for, 51, 52f

reciprocal, 48

recombination frequencies for, 121, 127–128, 133

testcrosses, 54, 58–60, 59f, 118–120, 119f, 124–127, 126f. See also Testcrosses

three-point, 129–136

two-point, 128–129

gene mapping with, 128–129

with unlinked genes, 60–62, 62t, 63f

Crossing over, 28f–29f, 29–32, 30t. See also Crosses; Crossovers

among three genes, 129–136

coupling configurations in, 122–124, 123f

definition of, 27, 29

dominance and, 48–49, 49f

genetic diversity and, 29–32

homologous recombination in, 250–251, 250f–251f

with incompletely linked genes, 120–121, 123–124

independent assortment and, 55–60, 56f, 116–117, 118f, 119f, 123–127, 126f

within inversions, 156–159, 158f

with linked genes, 117–127, 119f. See also Linked genes

mutations in, 152–153, 154f, 355–356, 356f

nonindependent assortment and, 116–117, 118f

as postreplication event, 250, 250f–251f

recombination frequencies and, 121, 127–128, 133

recombination in, 118f, 120–125. See also Recombination

repulsion and, 122, 123f

segregation in, 48–49, 51f, 52f, 116–117. See also Segregation

trans configuration in, 122, 123f

transformation and, 190

unequal, 152–153, 153f, 154f, 356, 356f

vs. translocation, 159

Crossovers

double, 128, 128f, 134–135, 137–138

coefficient of coincidence for, 134–135

four-strand, 137f, 138

within inversions, 156, 158

three-strand, 137f, 138

two-strand, 137–138, 137f

interference between, 134–135

location of, mapping of, 132–133, 133f

multiple, 137–138, 137f

predicted number of, 133

three-gene, 129–136, 130f

crRNA (CRISPR RNA), 262, 262t. See also RNA

Cultures

bacterial, 179f, 191

bacteriophage, 192, 193f

C-value, 226, 226t

C-value paradox, 226

Cyclic AMP, in catabolite repression, 320

Cyclin, 435

Cyclin-D–CDK, 435, 435f

Cyclin-dependent kinases, 435, 435f

Cyclin-E–CDK, 435, 435f

Cysteine, 291t

Cystic fibrosis, 476

inheritance of, 90

mutations in, 350

Cytochrome c, in evolutionary studies, 491

Cytokinesis, 23, 25t

Cytology, history of, 8–9

Cytoplasmic inheritance, 99–101, 100f, 100t, 102t

Cytosine, 215, 215f, 216–217, 216t, 217f. See also Base(s)

methylation of, 323. See also DNA methylation

Back to top ↑

dAMP (deoxyadenosine 5′ monophosphate), 216f, 216t

Danio rerio (zebrafish), 5–6, 6f

genome of, 416t

Darwin, Charles, 9, 459, 470, 486, 489

Darwin’s finches, allopatric speciation in, 486–487, 487f

Databases, bioinformatic, 410

Daughter chromosomes, formation of, 24f, 25, 26

Davenport, Charles, 43

Davenport, Gertrude, 43

Davis, Bernard, 184

Dawkins, Richard, 4

dCMP (deoxycytidine 5′ monophosphate), 216f, 216t

ddNTPs (dideoxyribonucleoside triphosphates), in DNA sequencing, 384–386, 384f, 386f

De Vries, Hugo, 44–45

Deacetylases, 324, 324f

Deacetylation, histone, in gene regulation, 324, 324f

Deamination

induced, 358, 358f

spontaneous, 356–357, 356f–357f

Death cap poisoning, 259–260

Degenerate code, 293–295

Deletions, 155–156, 155f, 155t, 156f, 170t, 347f, 348, 353t, 355–356, 355f, 356f

in cancer, 438

in-frame, 348, 353t

translocations and, 159

Denisovans, 409

Dentatorubral-pallidoluysian atrophy, 348t

Deoxyadenosine 5′ monophosphate (dAMP), 216f, 216t

Deoxycytidine 5′ monophosphate (dCMP), 216f, 216t

Deoxyguanosine 5′ monophosphate (dGMP), 216f, 216t

Deoxyribonucleoside triphosphates (dNTPs), in replication, 238–239, 239f, 384–386

Deoxyribonucleotides, 215, 216f, 216t

Deoxyribose, 214, 215f, 238–239

Deoxythymidine 5′ monophosphate (dTMP), 216f, 216t

Depurination, mutations and, 356, 357f

Development

gene regulation in, 4, 4f

RNA interference in, 328–329

dGMP (deoxyguanosine 5′ monophosphate), 216f, 216t

Diastrophic dysplasia, 3f

Dicentric bridges, 158

Dicentric chromatids, 158

Dicer, 279, 329

Dideoxy sequencing, 384–386, 384f–386f

Dideoxyribonucleoside triphosphate (ddNTP), in DNA sequencing, 384–386, 384f, 386f

Dihybrid crosses, 55–60, 56f, 58f, 59f

phenotypic ratios from, 96–98, 97t

Diploid cells, 21, 22f

Direct repair, 364

Directional selection, 482

Direct-to-consumer genetic tests, 395–396

Discontinuous characteristics, 104, 446–447, 446f

Discontinuous replication, 240, 240f

Diseases. See Genetic diseases

Dispersive replication, 234–235, 235f

Displaced duplications, 152

Distance approach, for evolutionary relationships, 489

Distributions, in statistical analysis, 451, 451f

Diver, C., 76

DNA, 11–12, 207–228

A form of, 218, 218f

ancient, 207–208

B form of, 218, 218f

bacterial, 19, 19f, 181, 181f, 191–192, 220f, 221, 221f

in bacteriophages, 211–212, 211f, 212f

bases in, 209, 209t, 214–215, 215f, 217f, 218f. See also Base(s)

during cell cycle, 23, 23f, 25t, 26, 26f, 435

cellular amounts of, 226, 226t

chloroplast, 100, 227. See also Chloroplast DNA (cpDNA)

circular, 181

bacterial, 181f

replication in, 248–249, 248f

coiling of, 21

damage to, repair of. See DNA repair

double helix of, 217–219, 218f

double-strand breaks in, 152, 250–251

early studies of, 208–209

essential characteristics of, 208

eukaryotic, 19, 19f, 221–224

functional, 227

as genetic material, 209–214

heteroduplex, 250

highly repetitive, 226–227

information transfer via, 218f, 219

linker, 223

as macromolecule, 214

measurement of, 26, 26f

microsatellite, in DNA fingerprinting, 389

mitochondrial, 99–100, 227. See also Mitochondrial DNA (mtDNA)

mobile. See Transposable elements

moderately repetitive, 226

noncoding, 416–417

nucleotides of, 214–215, 215f–217f

packaging of, 21, 220–225, 221f

in bacteria, 221, 221f

in eukaryotes, 220f, 221–224, 223f–225f

polynucleotide strands in. See Polynucleotide strands

prokaryotic, 19, 19f

in relaxed state, 220, 220f

repetitive, 226–227

replication of. See Replication

structure of, 214–219

discovery of, 213–214, 213f

genetic implications of, 219

hierarchical nature of, 220

primary, 214–216, 215f–217f, 220

secondary, 214, 216–219, 217f–219f, 220, 261t

tertiary, 220, 220f

tetranucleotide theory of, 209

vs. RNA structure, 260–261, 261t

Watson-Crick model of, 213–214, 213f, 219

supercoiling of, 220–221, 220f, 233–234

synthesis of. See Replication

in transformation, 189–190

as transforming principle, 210–212

in transposition, 362, 362f

unique-sequence, 226

unwinding of

in recombination, 250–251

in replication, 239–240, 239f–242f, 241–242

X-ray diffraction studies of, 213–214, 213f

Z form of, 218, 218f

DNA fingerprinting, 389–391, 390f, 390t

DNA gyrase, 241–242, 241f

DNA helicase, 241, 241f, 246f

in replication, 241, 241f, 246f

in Werner syndrome, 249–250

DNA libraries, 381–382

DNA ligase, 243–244, 244f, 246f

DNA methylation, 325

in cancer, 437

epigenetics and, 334, 334f, 336

in gene regulation, 325

in genomic imprinting, 103

RNA interference and, 329

DNA polymerase(s)

in DNA sequencing, 384–386

in mismatch repair, 364, 364f

in replication, 238–239, 242–250, 244t, 247

in bacteria, 242–245, 243t

in eukaryotes, 247

DNA probes, 376–377, 381–382

in DNA library screening, 381–382

DNA proofreading, 245

DNA repair, 364–365

base-excision, 364–365

cancer and, 435–436

in crossing-over, 28f, 29–32

direct, 364

in genetic diseases, 365, 365t

mismatch, 246, 364, 364f

nucleotide-excision, 365

in genetic disease, 365, 365t

SOS system in, 359

DNA sequences

functional role of, 227

types of, 226–227

DNA sequencing, 207, 384–386, 384–389

automated, 386, 386f

dideoxy (Sanger) method in, 384–386, 384f–386f

in gene mapping, 384–386, 384f–386f

in Human Genome Project, 406–409

illumina sequencing, 388–389, 388f

nanopore sequencing, 389

next-generation technologies in, 387–389, 387f, 409

pyrosequencing in, 387–388, 387f

restriction fragment length polymorphisms in, 383–384, 384f

third-generation technologies in, 389

DNA template

in replication, 234, 238–240, 239f, 240f

in transcription, 263f, 264, 264f

DNA transposons, 362. See also Transposable elements

DNA-binding proteins, 309, 323

dNTPs (deoxyribonucleoside triphosphates), in replication, 238–239, 239f, 384–386

Dobzhansky, Theodosius, 483

Dominance, 48–49, 49f, 89–90, 89f, 90t

characteristics of, 90

codominance and, 89–90, 89f, 90t

complete, 89, 89f, 90t

incomplete, 89, 89f, 90t

phenotype level and, 90

Dominance genetic variance, 455

Dominant epistasis, 95–96, 96f

Dominant traits

autosomal, 63, 65

inheritance of, 48–49, 65

Dosage compensation, 86–87

double Bar mutations, 153, 153f

Double crossovers, 128, 128f, 134–135, 137–138

coefficient of coincidence for, 134–135

within inversions, 158

Double fertilization, 35, 36f

Double helix, 216–218, 218f

Double-strand breaks, 152, 250–251

Down, John Langdon, 163

Down syndrome, 163–164

familial, 164, 164f

maternal age and, 164–165, 165f

primary, 163f, 164

Drosophila melanogaster (fruit fly)

Bar mutations in, 152–153, 153f

comparative genomics of, 417–418, 417f, 418t

eye color in, 81–82, 82f, 98, 129–135, 131f, 133f, 134f, 157

gene mapping for, 129–135, 131f, 133f, 134f

eye size in, 152–153, 153f

genetic map for, 129–135, 131f, 133f, 134f

genome of, 416, 416t, 417t

as model genetic organism, 5, 6f, 83–84, 83f

Notch mutation in, 156, 156f

pigmentation in, 492–493, 493f

sex determination in, 79–80, 79t

alternative splicing in, 327–328, 328f

X-linked characteristics in, 81–82, 82f

Drug development

genetics in, 3

recombinant DNA technology in, 395

Drug resistance, gene transfer and, 189

dTMP (deoxythymidine 5′ monophosphate), 216f, 216t

Duplications, 151f–153f, 152–154, 155t, 170t

displaced, 152

effects of, 152–153

in evolution, 154

gene, 493–494

reverse, 152

segmental, 154

tandem, 152

unbalanced gene dosage and, 153–154

whole-genome, 494

Back to top ↑

E site, 298, 298f, 299, 299f, 300f

East, Edward, 453–454

Edward syndrome, 164

Effective population size, 479

Elongation

in replication, 242–246

in translation, 298–299, 298f–299f, 301, 301t

Elongation factor G (EF-G), 298

Elongation factor Ts (EF-Ts), 298

Elongation factor Tu (EF-Tu), 298

ENCODE project, 227

Encyclopedia of DNA Elements, 227

Engineered nuclease, 375

Enhancer RNA (eRNA), 326

Enhancers, 325, 326, 327f

env gene, 199, 200

Environmental factors

in gene expression, 103–104, 103f

genotype-phenotype relationship and, 446–447. See also Genotype-phenotype relationship

in heritability, 456, 457

Environmental sex determination, 79

Environmental variance, 454

Enzyme(s). See also specific enzymes

deficiencies of, 103–104. See also Genetic diseases

gene expression and, 290

in recombination, 250–251

in replication, 241–242, 244t, 247. See also DNA polymerase(s)

restriction, 373–375

in translation, 296

Epialleles, 335

Epigenetic marks, 103, 334

Epigenetics, 11, 102–103, 224, 333–336

cancer and, 436–437

chromatin modification and, 224

definition of, 102, 224, 333

differences in twins and, 336

DNA methylation and, 334, 334f, 437

environmental chemicals and, 336

in gene expression, 224

histone modifications and, 334–335, 336

maternal behavior and, 335–336

molecular mechanisms in, 333–335

overview of, 333

paramutation and, 335, 335f

RNA and, 335

stress and, 335–336

Epigenome, 336

Episomes, 181

Epistasis, 94–95

dominant, 95–96, 96f

recessive, 94–95

Epistatic gene, 94

Epstein-Barr virus, cancer and, 439, 440, 440t

Equilibrium

for allelic frequencies, 477, 477f

Hardy-Weinberg, 473–476

Equilibrium density gradient centrifugation, 235–236, 235f

eRNA (enhancer RNA), 326

Escherichia coli (bacterium). See also Bacteria

antibiotic resistance in, 189

conjugation in, 182–189, 183f–188f, 187t. See also Conjugation

DNA polymerases in, 243–245, 244t

gene regulation in, 308–310

genetic techniques with, 191–192, 192f

genome of, 191, 192f

sequencing of, 414, 415t

in Hershey-Chase experiment, 211–212, 211f

lac operon in, 314–322

life cycle of, 191, 192f

as model genetic organism, 5, 6f, 191–192, 192f

operons in, 307–308. See also lac operon

partial diploid strains of, 316–317

replication in, 235–238, 237f

T2 bacteriophage in, 211–212, 211f

transformation in, 182, 183f, 189–190, 189f

tRNA in, 278

Ethical issues, in recombinant DNA technology, 409, 412

Ethylmethanesulfonate (EMS), as mutagen, 357, 358f, 359

Eubacteria, 19. See also Bacteria; Prokaryotes

genome of, 414, 415t

Euchromatin, 222

Eukaryotes, 11, 18f, 19–22, 19f

cell reproduction in, 21–22. See also Cell cycle

cell structure in, 18f, 19

definition of, 19

DNA in, 19, 19f, 221–224

genes of, 19, 414–419

genome of, 414–419, 416t

replication in, 237–238, 239t, 246–250

sexual reproduction in, 76, 77f

Evolution, 483

anagenesis, 483

biological, 483

chromosome rearrangements and, 156, 156f, 158

cladogenesis, 483–484

clonal, 430–431, 431f

Darwinian theory and, 9

duplications in, 154

gene regulation and, 492–493

as genetic change, 12

genetic drift in, 469–470

genetic variation and, 4, 27, 363, 469–470, 482–483. See also Population genetics

genome, 493–494, 493f

inversions in, 158

molecular clock and, 491–492, 492f

mutations in, 170

natural selection in, 459–461, 480–483. See also Natural selection; Selection

phylogenetic trees and, 489–490, 489f

polyploidy in, 170

rates of, 490–491

reproductive isolation in, 484, 486

response to selection in, 460–461

speciation in, 485–488. See also Speciation

of transposable elements, 363

as two-step process, 483

of viruses, 199–200, 199f

Exit (E) site, 298, 298f, 299, 300f

Exons, 272, 275, 276f

Expanding nucleotide repeats, 348–349, 348t, 349f, 353t

Expression vectors, 379, 379f

Expressivity, 91, 91f

Eye color, 81–82, 82f

in D. melanogaster, 81–82, 82f, 98, 157

gene mapping for, 129–135, 131f, 133f, 134f

Eye size, in D. melanogaster, 152–153, 153f

Back to top ↑

F′ cells, 186–187, 187t

F⁺ cells, 184–185, 185f–187f, 187t

F⁻ cells, 184–185, 185f–187f, 187, 187t

F factor, 181, 181f, 184–187, 185f–187f, 187t

F (filial) generations, in monohybrid crosses, 47f, 48, 49f

Familial Down syndrome, 164, 164f

Fanconi anemia, 365t

FBI, forensics and, 390–391

Feathering, in cocks vs. hens, 99

Federal Bureau of Investigation, 390

Fertility (F) factor, 181, 181f, 184–187, 185f–187f, 187t

Fertilization, 77f

in animals, 34–35, 34f

definition of, 27

double, 35, 36f

in plants, 35

Filial (F) generations, in monohybrid crosses, 47f

Finches, Darwin’s, allopatric speciation in, 486–487, 487f

Fire, Andrew, 279

Firmicutes, 411

First polar body, 34–35, 34f

Fisher, Ronald A., 448

Fitness, 481

5′ end (cap), 216, 274f, 275f

in replication, 239–240, 239f, 240f, 248, 248f, 249f

in transcription, 267f, 274, 328

in translation, 296f, 297

5′ splice site, 275–276, 276f

5′ untranslated region, 273, 273f

Fixation, allelic, 480

Flanking direct repeats, 361, 361f

FLC, 324

FLD, 324

Flower color

inheritance of, 89

lethal alleles and, 91

Flower length, inheritance of, 453–454, 453f

flowering locus C, 324

flowering locus D, 324

Flowering plants. See Angiosperms; Plants

Fly Room, 81f, 84

fMet-tRNA^fMet, 297

Follicular lymphoma, 436–437

Ford, Charles, 80

Forensics, DNA fingerprinting in, 389–391

Forward genetics, 391

Forward mutations, 349, 353t

Founder effect, 479

Four-o’clocks, cytoplasmic inheritance in, 100, 100f

Fragile sites, 160–161, 160f

Fragile-X syndrome, 160–161, 348, 348f, 348t, 349

Frameshift mutations, 348, 353t

in Ames test, 360

Franklin, Rosalind, 10, 213, 214

Free radicals, as mutagens, 359

Frequency distribution, 451, 451f

Friedreich ataxia, 348t

Fruit color, 93–94, 96f

Fruit fly. See Drosophila melanogaster (fruit fly)

Functional genetic analysis, 391–393

Functional genomics, 412–414

homology searches in, 412

microarrays in, 412–413, 413f

protein domains and, 417

Fusion proteins, in cancer, 438–439

Back to top ↑

G banding, 150, 151f

G overhang, 248

G₀ phase, 23, 23f, 25t

G₁ phase, 23, 23f, 25t

G₁/S checkpoint, 23, 23f, 435, 435f

G₂ phase, 23, 23f, 25t

G₂/M checkpoint, 23, 23f

G6PD deficiency, 103–104

gag gene, 199, 200

Gain-of-function mutations, 350, 353t

ß-Galactosidase, 307

Galápagos Islands, Darwin’s finches of, 486–487

Gallo, Robert, 199

Galton, Francis, 448

Gametes

nonrecombinant (parental), 119f, 120

recombinant, 119f, 120

size of, 77

unbalanced, 167

Gametophytes, 35, 35f

Garrod, Archibald, 1, 271, 290

GDP (guanosine diphosphate), in translation, 298

Gel electrophoresis, 375–376, 375f

in restriction mapping, 405

Gene(s). See also Genome(s); Protein(s) and specific genes

allelic, 11, 46. See also Alleles

bacterial, 19, 19f, 180–181, 181f, 191, 192f

number of, 414, 415t

cloning of, 377–379. See also Cloning

coding vs. noncoding regions of, 271–272

colinearity with proteins, 271–272

constitutive, 309

definition of, 46, 46t, 273

distance between, recombination frequencies and, 127, 133

dosage of, 153–154

duplication of, 493–494

epistatic, 94

eukaryotic, 19, 414–419

evolution of, 493–494, 493f

functionally related, 310. See also Operons

functions of

DNA sequence and, 412. See also Functional genomics

in humans, 417, 418f

in prokaryotes, 415f

as fundamental unit of heredity, 11

haploinsufficient, 156, 434

homologous, 412

hypostatic, 94

identification of, functional genomic techniques for, 412–414. See also Functional genomics

interrupted, 271–272

isolation of, molecular techniques for, 381–383

jumping. See Transposable elements

linked, 117–127. See also Linkage; Linked genes

location of. See Gene loci

movable. See Transposable elements

nucleotide substitutions in, 490–491, 490t

oncogenes, 199, 432–433

organization of, 271–272, 271f

prokaryotic, 19–20, 414, 415t

pseudogenes, 491

regulator, 310

regulatory, 309

mutations in, 318f

size of, in humans, 418–419, 418f

structural, 309, 310. See also Operons

mutations in, 316–320

structure of, 271–272

tumor-suppressor, 432, 433–434, 433f

viral, 20, 20f

vs. traits, 11. See also Genotype-phenotype relationship

Gene cloning. See Cloning

Gene density, 226, 227, 418

Gene deserts, 416–417

Gene expression, 4, 4f

chromatin structure and, 323

enzymes and, 290

epistatic, 94–98

expressivity in, 91, 91f

functional genomics and, 412–414. See also Functional genomics

genomic imprinting and, 102–103, 102t

microarrays and, 412–414, 413f

penetrance in, 90–91, 91f

phenotype and. See Genotype-phenotype relationship

regulation of. See Gene regulation

Gene families, 226

Gene flow (migration), 477–478, 478f

allelic frequency and, 478f, 482–483, 482t

Gene interaction, 93–98

definition of, 93

epistasis and, 94–98

novel phenotypes from, 92f, 93–94

phenotypic ratios from, 96–98, 97t

Gene interaction variance, 455

Gene loci, 12, 46, 46t

methods of finding, 381–383. See also Gene mapping

quantitative trait, 458–459, 459t

Gene mapping, 115–140

in bacteria, 194–196, 197f

in bacteriophages, 197

Benzer’s technique for, 198

coefficient of coincidence in, 134–135

with cotransformation, 190f

crossover locations in, 132–133, 133f

in D. melanogaster, 129–135, 131f, 133f, 134f

DNA sequencing in, 384–386, 384f–386f

double crossovers and, 128, 128f, 134–135, 137–138

in eukaryotes, 115–140

gene order in, 131–132

genetic maps in, 127–138, 404, 405f

genetic markers in, 138

genome sequencing and, 406–409

genome-wide association studies in, 138–139, 139f, 410, 459

historical perspective on, 116–117

in humans, 137–138

interference in, 134–135

with interrupted conjugation, 187–188, 188f, 195–196

linkage analysis in, 127–139, 139f, 404, 405f. See also Linkage analysis

map units for, 127, 404

in phages, 197–198

physical maps in, 127, 404–405, 406f

quantitative trait loci in, 445–446, 458–459, 459t

recombination frequencies in, 127–128, 133, 404

restriction, 405

restriction fragment length polymorphisms in, 383–384, 384f

single-nucleotide polymorphisms in, 409–410

with three-point testcrosses, 129–136

with transduction, 194–196, 197f

with transformation, 190, 190f, 195–196

with two-point testcrosses, 128–129

in viruses, 197–198

Gene microarrays, 412–414, 413f, 414f

Gene mutations, 347. See also Mutation(s)

Gene pool, 470

Gene regulation. See also Gene expression

alternative splicing in, 327–328, 328f

in bacteria, 307–322

vs. in eukaryotes, 322, 330–331

boundary elements in, 326–327, 327f

catabolite repression and, 320

chromatin structure and, 322–325

coactivators in, 325–326

coordinate induction in, 315

coordinated, 327

definition of, 308

in development, 4, 4f

DNA methylation in, 325

DNA-binding proteins in, 323

enhancers in, 325, 327f

in eukaryotes, 308–310, 322–333

vs. in bacteria, 322, 330–331

evolution and, 492–493

histone acetylation in, 323–324, 323f

inducers in, 311

insulators in, 326–327, 327f

levels of, 309–310, 312f

mRNA processing in, 327–328, 329f

negative, 309, 311–312, 312f, 313f, 314f

operators in, 310, 311f

operons in, 310–322

lac, 314–322, 315f

overview of, 308–310

positive, 309, 311, 312–313, 314f

posttranslational, 329–330

regulatory elements in, 309

repressors in, 315, 326. See also Repressors

response elements in, 327

RNA interference (silencing) in, 326, 329, 393

transcriptional, 309–310, 309f

translational, 329–330

transposable elements in, 362–363

Gene therapy, 4, 396

for Leber congenital amaurosis, 371–372

Gene transfer

antibiotic resistance and, 189

bacterial, 182–192, 494

in biotechnology. See Recombinant DNA technology

by conjugation, 182–189, 183f–188f, 187t, 195–196

horizontal, 191, 494

by transduction, 182, 183f, 194–195, 195f, 196f

by transformation, 182, 183f, 189f, 190, 195–196

Gene vectors. See Cloning vectors

Gene-environment interactions, 103–104, 103f. See also Epigenetics

General transcription factors, 325

Generalized transduction, 194–195, 196f. See also Transduction

Genetic analysis, functional, 391–393

Genetic bottleneck, 479

Genetic code, 291–295

amino acids in, 291–295, 293f, 294f

in bacteria vs. eukaryotes, 301

breaking of, 291–293

codons in, 292–295, 294f. See also Codons

degeneracy of, 293–295

diagram of, 294f

exceptions to, 295

nonoverlapping, 294

reading frames for, 295, 348

triplet, 292

universality of, 295

Genetic crosses. See Crosses

Genetic diagnosis. See Genetic testing

Genetic differentiation, speciation and, 485–488. See also Speciation

Genetic diseases

albinism, 1–2

Bowen-Conradi syndrome, 289–290

cancer as, 429–431

cystic fibrosis, 90, 350, 476

diastrophic dysplasia, 3f

direct-to-consumer tests for, 395–396

environmental factors in, 104

expanding nucleotide repeats in, 348–349, 348t

faulty DNA repair in, 365, 365t

fragile-X syndrome, 160–161, 348, 348f, 348t, 349

gene therapy for, 4

genetic testing for, 395–396

genome-wide association studies for, 138–139, 410, 459

genomic imprinting and, 102–103, 102t

Klinefelter syndrome, 87, 163

Leber congenital amaurosis, 371–372

Leber hereditary optic neuropathy, 101

mitochondrial, 100–101

neurofibromatosis, 159

pedigree analysis for, 63–65, 64f, 65f

single-nucleotide polymorphisms in, 409–410

telomerase and, 249–250

transposable elements in, 362–363

Turner syndrome, 87, 163

Waardenburg syndrome, 63, 65f

xeroderma pigmentosum, 365, 365f, 365t, 430–431

Genetic dissection, 346

Genetic diversity. See Genetic variation

Genetic drift, 469–470, 478–480, 479f, 482–483, 482t

allelic frequencies and, 479–480, 479f, 482t

causes of, 479

definition of, 479

effects of, 479–480, 482t

magnitude of, 479

Genetic engineering, 372, 394–396. See also Recombinant DNA technology

Genetic maps, 127–138, 404, 405f. See also Gene mapping

Genetic markers

in gene mapping, 138

Y-linked, 87–88

Genetic material

candidate, 209

DNA as, 209–214

early studies of, 208–209

essential characteristics of, 208, 219

protein as, 209

RNA as, 214

Genetic maternal effect, 101, 101f, 102t

Genetic mutations. See Mutation(s)

Genetic recombination. See Recombination

Genetic rescue, 470

Genetic studies, 63–65

bacteria in, 178t. See also Bacteria

human

difficulties in, 63

pedigree analysis, 63–65

model organisms for, 5–7, 6f, 7f. See also Model genetic organisms

viruses in, 178t. See also Viruses

Genetic testing, 395–396

Genetic variance, 454. See also Variance

additive, 455

dominance, 455

Genetic variation, 4, 363, 470

allelic fixation and, 479–480

chromosome distribution and, 31, 31f

crossing over and, 29–32

evolution and, 4, 363, 482–483

genetic drift and, 478–480

loss of, 469–470

meiosis and, 29–32

migration and, 477–478, 478f

mutations and, 363, 476–477, 477f. See also Mutation(s)

recombination and, 250–251

sexual reproduction and, 29–32

sources of, 29–32

universality of, 470

Genetically modified plants, 3, 3f, 395

Genetic-environmental interaction variance, 454–455, 454f

Genetics

applications of, 3–4, 10–11

in agriculture, 3, 3f, 7–8, 7f

in biotechnology, 3

commercial, 3

in medicine, 4, 10

in pharmaceutical industry, 3

basic concepts of, 2–7, 11–12

biology and, 4

divisions of, 5, 5f

evolution and, 4, 9, 12

forward, 391

future of, 10–11

historical perspective on, 7–10, 9t

importance of, 2–7

model organisms in, 5–7, 6f, 7f. See also Model genetic organisms

in modern era, 10–11

molecular, 3f, 5, 5f

notation in. See Notation

population, 5, 5f. See also Population genetics

quantitative, 445–446. See also Quantitative genetics

reverse, 391

transmission, 5, 5f

universality of, 4

viral, 193–201

Genic sex determination, 78–79

Genome(s). See also Gene(s)

of Arabidopsis thaliana, 332, 332f, 416, 416t, 417t

of bacteria, 18f, 19, 180–181, 183f, 191, 192f

sequencing of, 414, 415t

size of, 414, 415t

of Bradyrhizobium japonicum, 414, 415t

of Caenorhabditis elegans, 281–282, 416

definition of, 4

doubling of, 170

duplication of, 494

of Escherichia coli, 414

of eukaryotes, 18f, 414–419, 416t, 417t

evolution of, 493–494, 493f

of Homo sapiens, 418–419

of honeybees, 403–404

of Mus musculus, 394f

of plants, 416, 416t, 417t

of prokaryotes, 414, 415t

sequencing of, 10–11, 10f, 227, 406–409

ENCODE project for, 227

ethical aspects of, 409

in Human Genome Project, 406–409

map-based, 406–407, 407f

metagenomics and, 411

single-nucleotide polymorphisms in, 409–410, 410f

whole-genome shotgun, 407–408, 408f

size of, 226, 226t

in prokaryotes, 414, 415t

of viruses, 193, 193f

of yeast, 416t, 417t

Genome-wide association studies, 138–139, 139f, 410, 459

Genomic imprinting, 102–103, 102f, 102t

epigenetics and, 102–103

Genomic instability, in cancer, 439

Genomic libraries, 381–382

Genomics, 403–421

comparative, 414–419

definition of, 404

ethical issues in, 409

functional, 412–414. See also Functional genomics

structural, 404–412. See also Structural genomics

Genotype, 11, 46, 46t

expression of. See Gene expression

inheritance of, 46. See also Inheritance

Genotype-phenotype relationship, 11, 46–47. See also Gene expression

continuous characteristics and, 104

cytoplasmic inheritance and, 99–101, 100f, 100t

environmental influences on, 103–104, 103f, 454–455

expressivity and, 91, 91f

gene interaction and, 93–98. See also Gene interaction

genetic maternal effect and, 101, 101f

genetic variation and, 470. See also Genetic variation

heritability and, 454–455

mutations and, 355–356

one-gene–one-enzyme hypothesis and, 290

one-gene–one-polypeptide hypothesis and, 290

penetrance and, 90–91, 91f

polygenic inheritance and, 448–450, 450f

quantitative traits and, 446–447, 447t, 448f

sex influences on, 98–103, 102t

Genotypic frequency

calculation of, 471

Hardy-Weinberg law and, 473–474

nonrandom mating and, 476

Genotypic ratios, 55, 55t

observed vs. expected, 60–62, 63f

Germ-line gene therapy, 396

Germ-line mutations, 347, 347f

Germ-plasm theory, 8f, 9, 9t

Gibson, Daniel, 411

Globin genes, evolution of, 493–494, 493f

Glucose metabolism, catabolite repression and, 320

Glucose-6-phosphate dehydrogenase (G6PD) deficiency, 103–104

Glutamate, 291t

Glutamine, 291t

Glycine, 291t

Goats, bearding of, 99

Goodness-of-fit chi-square test, 61–62, 62t, 63f

for crosses/linkages, 61–62, 62t, 63f, 126f

for Hardy-Weinberg proportions, 475

for independent assortment, 125, 126–127

Green fluorescent protein, 283, 283f

Green Revolution, 3, 3f

Gret1 retrotransposon, 363

Grew, Nehemiah, 8

G-rich strand, of telomere, 225, 225f

Griffith, Fred, 209–210

Guanine, 214–215, 215f, 216–217, 216t, 217f. See also Base(s)

Guanosine diphosphate (GDP), in translation, 298

Guanosine triphosphate (GTP), in translation, 296, 298

Gut microflora, obesity and, 411

Gyrase, 241–242, 241f

Back to top ↑

H3K4me3, 323

H3K27me3, 335

Hair color, inheritance of, 43–44

Hairpins, 270, 280

nucleotide repeats and, 349, 349f

Hamkalo, Barbara, 263

Haploid cells, 21

Haploinsufficiency, 156, 434

Haplotypes, 139, 409–410, 410f

Hardy, Godfrey H., 474

Hardy-Weinberg equilibrium, 473, 475

Hardy-Weinberg law, 473–476

allelic frequencies and, 473–474

assumptions of, 473, 474

genotypic frequencies and, 473–474

implications of, 474

statement of, 473

H-DNA, 218

Heart disease, congenital, 345

Heat-shock proteins, 327

Helicase, in replication, 241, 241f, 246f

in Werner syndrome, 249–250

Helix

alpha, 218f, 291, 292f

double, 216–218, 218f

Helper T cells, in HIV infection, 200f

Hemings, Sally, 88

Hemizygosity

definition of, 82

X chromosome inactivation and, 86–87

Hen feathering, 99

Hereditary nonpolyposis colon cancer, 365t

Heredity. See also Inheritance

chromosome theory of, 50–51, 117

gene as fundamental unit of, 11

molecular basis of. See DNA; RNA

principles of, 43–66

sex influences on, 98–103, 102t

Heritability, 454–459

broad-sense, 455

calculation of, 455–456

definition of, 454

environmental factors in, 456, 457

of intelligence, 458

limitations of, 456–458, 458t

narrow-sense, 455, 460

phenotypic variance and, 454–455

population differences and, 457

realized, 460

response to selection and, 460–461

specificity of, 457

summary equation for, 455

Hershey, Alfred, 197, 211–212

Hershey-Chase experiment, 211–212, 211f

Heterochromatin, 222

Heteroduplex DNA, 250

Heterogametic sex, 77

Heterozygosity

autosomal recessive traits and, 65, 65f

definition of, 46, 46t

dominance and, 89, 89f

loss of, in cancer, 434, 434f

nonrandom mating and, 476

Heterozygotes, compound, 93

Hfr cells, 185–186, 187t

Highly repetitive DNA, 226–227

Hillmer, Axel, 115–116

Histidine, 291t

Histone(s), 19, 19f, 21, 222–223

acetylation/deacetylation of, 323–325, 323f, 324f

in cancer, 437

epigenetics and, 334–335, 336, 437

methylation of, 323

in cancer, 437

epigenetics and, 334, 336, 437

in nucleosome, 222–223, 223f

Histone code, 323

Histone demethylases, 323

Histone methyltransferases, 323

HIV (human immunodeficiency virus infection), 199–200, 199f, 200f

Holandric traits. See Y-linked characteristics

Holliday intermediate, 251

Holliday junction, 250–251, 250f–251f

Holliday model, 250f–251f

Holoenzymes, 266

Homo sapiens. See under Human

Homogametic sex, 77

Homologous characteristics, 488–490

Homologous genes, 412

Homologous pairs of chromosomes, 21, 21f, 29–32

separation of, 31, 31f, 33–34, 33f, 50–51

Homologous recombination, 250–251, 250f–251f

Homozygosity

autosomal recessive traits and, 65, 65f

definition of, 46, 46t

dominance and, 89, 89f

inbreeding and, 476

nonrandom mating and, 476

Homunculus, 8, 9f

Honeybees, genome of, 403–404

Hooke, Robert, 8

Hopi, albinism in, 1–2, 2f

Hoppe-Seyler, Ernst Felix, 208

Horizontal gene transfer, 191, 494

HPV (human papillomavirus), cervical cancer and, 440

Hrdlieka, Ales, 1

HTLV-1, 440t

Human genetic studies, 63–65. See also Genetic studies

Human genome, 416t, 417t, 418–419

sequencing of, 10, 406–409

Human Genome Project, 10, 406–409

Human immunodeficiency virus (HIV), 199–200, 199f, 200f

Human papillomavirus (HPV), cervical cancer and, 440

Human Proteome Project, 419

Huntington disease, 348t, 349

gene mapping in, 384, 384f

Hutterites, Bowen-Conradi syndrome in, 289–290

Hybridization. See also Breeding

allopolyploidy and, 167–168, 168f

of plants, 7–8

Hydrogen bonds, in DNA, 216–217, 217f

Hydroxylamine, as mutagen, 358–359, 358f

Hypostatic gene, 94

Back to top ↑

Igoshin, Oleg, 307–308

Illumina sequencing, 388–389, 388f

Immunodeficiency states, 199–200

Inbreeding, 476

Inbreeding depression, 476

Incomplete dominance, 89f, 90, 90t, 91f

Incomplete linkage, 119f, 120–121, 123–124

Incomplete penetrance, 90, 91f

Incorporated errors, 355

Independent assortment, 31, 55–60, 56f, 93, 116–117, 123–127

chi-square goodness-of-fit test for, 125–127, 126f

interchromosomal recombination and, 124. See also Recombination

principle of, 55

testcrosses for, 124–127, 126f

vs. complete linkage, 118–120, 119f

vs. nonindependent assortment, 117, 118f

Induced mutations, 354, 357–359. See also Mutation(s)

Inducers, 311

Inducible operons

negative, 311–312, 312f, 314f

lac operon as, 314–315

positive, 312–313, 314f

Induction, coordinate, 315

Influenza virus, 200–201, 200t

In-frame deletions, 348, 353t

In-frame insertions, 348, 353t

Inheritance, 43–66. See also Heredity

of acquired characteristics, 8, 9, 9t, 47

blending, 8, 9t

chromosome theory of, 50–51, 116–117

codominance in, 89–90, 90t

complete dominance in, 89

of continuous characteristics, 104

cytoplasmic, 99–101, 100f, 100t, 102t

of dominant traits, 48–49, 49f, 63, 65, 65f, 89–90, 89f, 90t

early concepts of, 7–10, 9t

gene interactions and, 93–98

of genotype vs. phenotype, 47

incomplete dominance in, 89, 89f

incomplete penetrance in, 90–91, 91f

of linked genes, 115–140. See also Linkage; Recombination

Mendelian, 8, 9t, 10, 44–51

in monohybrid crosses, 47–55. See also Monohybrid crosses

polygenic, 448–450

of quantitative characteristics, 448–450, 450f

of recessive traits, 48–49, 65, 65f

segregation in, 50–51, 52f, 116–117

sex-linked, 76–88, 81–88. See also Sex-linked characteristics

studies of. See Genetic studies

Initiation (start) codons, 273, 295

Initiation factors, in translation, 296–298, 297f, 330

Initiator proteins, 240, 241f

Insertions, 347f, 348, 353t, 355–356, 355f, 356f

in-frame, 348, 353t

Insulators, 326–327, 327f

Integrase, 199

Intelligence, heritability of, 458

Intercalating agents, as mutagens, 359, 359f

Interchromosomal recombination, 124

Interference, 134–135

Intergenic suppressor mutations, 352–353, 352f, 353t

Interkinesis, 28, 30t

Interphase, 22–23. See also Cell cycle

meiosis and, 27, 28f, 30t

mitosis and, 23–25, 23f, 24f, 25t

Interrupted conjugation, in gene mapping, 187–188, 188f

Interrupted genes, 271–272

Interspersed repeat sequences, 226

Intrachromosomal recombination, 124

Intragenic suppressor mutations, 350–352, 351f, 353t

Introns, 272, 272f

self-splicing. See Splicing

size of, in humans, 418, 418f

Inversions, 156–159, 170t

in cancer, 438–439

in evolution, 158

in meiosis, 157–158, 158f

paracentric, 156, 157f, 170t

pericentric, 156, 156f, 158, 158f, 170t

phenotypic effects of, 156

Inverted repeats, 361f

terminal, 362

Ionizing radiation, 359

IQ, heritability of, 458

Isoaccepting tRNA, 293

Isoleucine, 291t

Isotopes, 211–212

Back to top ↑

Jacob, François, 188, 307, 314, 316–317

Jacobsen syndrome, 348t

Jefferson, Thomas, 88

Johannsen, Wilhelm, 46, 448

Jumping genes. See Transposable elements

Back to top ↑

Karpechenko, George, 168

Karyotypes, 150

definition of, 150

human, 150, 151f

preparation of, 150–151

Kinases, cyclin-dependent, 435, 435f

Kinetochores, 22, 22f, 24

Klinefelter syndrome, 80, 80t, 87, 163

Knock-in mice, 392

Knockout mice, 392

Knudson’s multistep cancer model, 429–430, 430f

Kossel, Albrecht, 208, 213

Kozak sequence, 297

Back to top ↑

lac enzymes, induction of, 314–315

lac mutations, 316–320, 318f

operator, 317, 318f

regulator-gene, 317

structural-gene, 316–320, 318f

lac operon, 307, 314–322, 315f, 316f. See also Operons

catabolite repression and, 320

mutations in, 316–320, 318f

regulation of, 314–315, 316f

lac promoter, 315

mutations in, 317–320

lac repressors, 315, 315f, 316f

lacA gene, 315, 315f, 317

lacI gene, 315, 317, 318f

lacO gene, 317

lacP gene, 315, 315f

Lactose, 314, 315f

metabolism of, 314–322

lacY gene, 315, 315f, 317

lacZ gene, 315, 315f, 317, 318f

in cloning, 378, 378f

mutations in, 316–320

Lagging strand, 240, 240f

Lambda (l)phage, 379, 379t. See also Bacteriophage(s)

Large ribosomal subunit, 279

Lariat, 275, 276f

Leading strand, 240, 240f

Leaf variegation, cytoplasmic inheritance and, 100, 100f

Leber congenital amaurosis, 371–372

Leber hereditary optic neuropathy, 101

Lederberg, Joshua, 182–184, 194

Lederberg-Zinder experiment, 194

Lethal alleles, 91–92

Lethal mutations, 163, 350, 353t

Leucine, 291t

Leukemia, 438–439, 439f

Levene, Phoebus Aaron, 209, 213

Libraries

DNA, 381–382

genomic, 381

Li-Fraumeni syndrome, 365t

Ligase, in replication, 243–244, 244f, 246f

Limnaea peregra (snail), shell coiling in, 75–76, 101, 101f

Linear eukaryotic replication, 237–238, 238f, 239t

LINEs (long interspersed elements), 226

Linkage

chi-square goodness-of-fit test for, 61–62, 62t, 63f, 125–127

complete, 118–120, 119f, 123–124

incomplete, 119f, 120–121, 123–124

independent assortment and, 118–120, 119f

testcross for, 118–120, 119f

three-gene, 129–136

Linkage analysis, 127–139, 404, 405f. See also Gene mapping

definition of, 138

in humans, 137–138

single-nucleotide polymorphisms in, 409–410, 410f

Linkage disequilibrium, 139

Linkage groups, 117

in two-point crosses, 128–129

Linkage maps. See Genetic maps

Linked genes, 117–127

complete linkage of, 118–120, 119f, 123–124

crosses with, 117–127. See also Crosses

coupling in, 122–124, 123f

notation for, 118

predicting outcome of, 124–125

recombination frequency for, 121

in repulsion, 122, 123f

testcrosses for, 118–120, 119f

crossing over with, 119f, 120–121, 120f

definition of, 117

incomplete linkage of, 119f, 120–121, 123–124

recombination frequency for, 121

Linker DNA, 223

Lipton, Mary, 420

lncRNA (long noncoding RNA), 262, 262t, 281. See also RNA

Locus, gene, 12, 46, 46t

methods of finding, 381–383. See also Gene mapping

quantitative trait, 448–450, 458–459, 459t

Long interspersed elements, 226

Long noncoding RNA (lncRNA), 262, 262t, 281. See also RNA

Loss of heterozygosity, in cancer, 434, 434f

Loss-of-function mutations, 350, 353t

Lung cancer, 432

Lwoff, Andre, 307

Lymphocytes, in HIV infection, 200

Lymphoma

Burkitt, 439, 439f, 440

follicular, 436–437

Lyon hypothesis, 86

Lysine, 291t

Lysogenic life cycle, viral, 193, 193f

Lytic life cycle, viral, 193, 193f

Back to top ↑

‘M phase

in cell cycle, 23–25, 23f, 24f, 25t, 26. See also Mitosis

of cell cycle, 23–25

MacLeod, Colin, 210–211

Malignant tumors, 429. See also Cancer

Map unit (m.u.), 127, 404

Map-based sequencing, 406–407, 407f

Mapping functions, 137f, 138

Maps. See Gene mapping

Markers, Y-linked, 87–88

Mass spectrometry, in proteomics, 419–420, 419f

Maternal age, aneuploidy and, 164–165, 165f

Maternal behavior, epigenetics and, 335–336

Mathematical models, in population genetics, 472–473

Mating

assortive, in sympatric speciation, 488

nonrandom, 476

Matthaei, Johann Heinrich, 292

Mayr, Ernst, 484, 488

McCarty, Maclyn, 210–211

McClintock, Barbara, 225

Mean, 452, 452f

Media, culture, 179f

Medicine, genetics in, 4, 10. See also Genetic diseases

Megaspores, 35, 36f

Megasporocytes, 35, 36f

Meiosis, 12, 27–37, 30f–32f

in animals, 34–35, 34f

cell division in, 26f, 27

crossing over in, 27, 28f–29f, 29–32, 30t, 50–51

definition of, 27

genetic consequences of, 29–32, 30f, 31f

genetic crosses and, 50–51

genetic variation and, 29–32

independent assortment in, 56, 56f

inversions in, 156–159, 158f

overview of, 27–29, 28f–29f

in plants, 35, 36f

regulation of, 435

segregation in, 50–51, 52f, 116–117