This is a free sample of content from Decoding the Language of Genetics. Click here for more information or to buy the book. Index A Andrews, Brenda J., 135–136 Annotation, genome, 167 ABO locus, 19 Anticodon, 92, 115 Actin, 121–122, 127, 134 Anti-correlation coefficient, 38 Activation, 67 Antimorph, 27 Activator, 157 Antitermination, 149 AraC, 148–149, 151–152 Arabinose (ara) operon in E. coli, 148–150, catabolite activator protein (CAP), 150 151–152 Adams, Alison E.M., 122, 128 AraC, 148–149, 151–152 Adaptors, 92, 104 Arginine biosynthesis, 124–125, 124f Adenosine triphosphate (ATP), 47 Autozygosity, 186 AFLPs (amplified fragment length Auxotrophs, 49–50, 53, 106–112, 131 polymorphisms), 12 Age-related macular degeneration, 203 B Agglutination of red blood cells, 19 Alkaptonuria, 185–186 Backcross, 18 Allele frequencies, 183 Back mutation, 105 Alleles, 12–14 Bacteria, coupling of transcription inferring human gene function from and translation, 139 disease alleles, 195–206 Bacteriophage l, 118–119 mutant, 13, 20–22, 24–27 Bacteriophage T4 null, 14, 26, 28–29 genome, 71–73 pseudoalleles, 28 infection process, 71 wild-type, 13–14 morphogenesis and assembly pathways, 52– Allelism, 12–13, 38 55, 54f Allelomorph, 12 protein biosynthesis regulation, 138 rII Allosteric activation, 64 system, 72 Allosteric inhibition, 63 fine-structure mapping, 78–80 Allosteric interaction, mutations affecting, 200– mutations, 71, 74, 78–81, 95, 107, 201 111–112, 114 Allosteric modulation, 64 polycistronic mRNA, 144 Amber mutations, 110 r phenotypes, 75 Ameliorating interaction, 134 Balanced reciprocal translocations, 97 Amino acids Base-pairing, 88, 92–93 genetic code, 87, 91–92, 92t Bateson, William, 8, 12, 15, 57, 133, 184–185 in metabolic pathways, 61 Benzer, Seymour, 6, 12, 17 number in typical proteins, 94 biography, 84 Amorph, 27 cis–trans test, 81–83, 82f Amplified fragment length polymorphisms function gene definition, 81–83, 84 (AFLPs), 12 phage studies by, 71–74, 78–81, 83, 95, 111 ___ 211 © 2015 Cold Spring Harbor Laboratory Press. All rights reserved. This is a free sample of content from Decoding the Language of Genetics. Click here for more information or to buy the book. 212 INDEX Bernard, Claude, 69 Chromosomes b-galactosidase, 141, 143–146, 159, 207 gain and loss of entire, 162 b-galactoside permease, 141, 143–145 recombination, 100–103, 102f b-galactoside transacetylase, 141, 143–145 translocations, 97–98, 98f, 161–162 b-globin genes/proteins, 20–22, 172–173 cis-acting elements, regulation and, 156–157, Biochemical reactions, 47. See also Metabolic 162 pathways cis-acting regulatory sites, 177, 202 Biotechnology, 157–160 cis-dominance, 114, 145–146, 157 Blood types, human, 19 cis–trans test, 17, 114 Boone, Charlie M., 135–136 Benzer and, 81–83, 82f BRCA1 alleles, 23–24 cis-dominance, 145–146 Breast cancer, 23–24 Lewis and Pontecorvo, 81, 84 Brenner, Sydney, 114–115 Cistron, 91 Bridges, Calvin, 97, 104 cis–trans test and, 17, 82–83 Brown, Michael, 198, 206 defined, 82–84 Bypass suppressors, 124–125, 124f polycistronic messenger RNA (mRNA), 142 Coding strand, 87, 92–93, 139 CODIS, 11–12 C Codominance, 19, 21, 36 Caenorhabditis elegans, sex determination in, Codons, 87, 91–92, 92f 127 Coinfections, phage, 75–76, 78 CAG repeats, 199, 205–206 Cold-sensitive (Cs) mutations, 119–121 cAMP (cyclic AMP), 150 Combinatorial regulation, 150–151 Cancer Combined DNA Index System (CODIS), amplification of genomic sequences, 101 11–12 applications of genetics and Complementation, 13, 27–29 genomics, 209 Complementation group, 28 causative mutation, 10 Complementation tests. See also cis–trans test loss of heterozygosity and, 201–202 araC cistron, 151 oncogenes, 175, 200 in phage crosses, 75 point mutations and, 175 suppressor mutations and, 120, 125 TP53 gene mutation, 14 T4 conditional-lethal mutants, 53 translocations and, 98, 162 Complement factor H, 203 tumor cell selection assays, 161–163 Complex phenotypes, 131–136 tumor-suppressor genes, 102, 162, 175, 196, disease phenotypes, 203–205 200, 201–202, 206 epistasis, 133 virus integration into genome, 100 gene interactions, 134 Cannon, Walter, 68–69 genetic heterogeneity, 131–132 Catabolite activator protein (CAP), 150, 155 genome-scale genetic interactions in yeast, Catalysis, by enzymes, 47, 48, 49f 134–136, 135f CCR5 gene, 210 polygenic inheritance, 132 Cell cycle, 123 quantitative traits, 132 Centimorgan, 37 synthetic phenotypes, 132–133 Chain-termination mutations, 96 Compound heterozygote, 27–29 Chaperone protein, 118 Conditional-lethal mutations, 52–53, 74–75, 77, Chemokine receptor, 210 107, 119–120, 122–123 Chemostat, 62 Consanguinity, 184 Chlamydomonas reinhardtii, flagella of, Conserved DNA 125–126 conservation of functional sequences, Cholesterol homeostasis, 210 167–169 Chorismic acid, 63, 63f phenotypic effects of mutations in, Chromosomal rearrangements, 161–162, 171 174–179 © 2015 Cold Spring Harbor Laboratory Press. All rights reserved. This is a free sample of content from Decoding the Language of Genetics. Click here for more information or to buy the book. INDEX 213 Constitutive, 141 haplotype, 42–43 Constitutive mutants, 141 in TP53 gene, 14 Lac system, 141, 143–145 linkage mapping, 11, 196 Copy number variants (CNVs), 98–99, 161–162, linkage phase, 42, 43f 171, 202, 205 segregation of polymorphic loci Corepressors, 148, 155 single locus, 39–40, 39f Correns, Carl Erich, 15 three loci, 41, 41f Crick, Francis, 92, 100, 104, 114 two loci, 40, 40f Cross-feeding, 50–51, 51f, 55, 56 DNA recombination. See Recombination Crossing over, 31, 34, 34f, 36, 101, 102f, DNA repair, 101, 103 187–189 DNA sequence variant, 10, 11 Cyclic AMP (cAMP), 150 DNA variants, 9–14 Cyclins, 123 alleles, 12–14 Cystic fibrosis, 44, 183 mutations, 9–10 Cytological analysis, 97 polymorphisms, 10–12 Cytoskeleton, 121–122, 125–126 Dobzhansky, Theodosius, 1, 14, 132 Domain architecture of proteins and their genes, 163–166, 164f D Dominance, 17–22, 24–27 biological interpretation of, 24–27 Darwin, Charles, 10, 15 cis-dominance, 114, 145–146, 157 Databases codominance, 19, 21 genome sequences, 167 definition, 18 human mutations, 14, 175 gain-of-function, 25 Degeneracy, genetic code, 91–92, 177 genomic rearrangements and, 202 Delbru¨ ck, Max, 84 Deletions (deletion mutations), 13–14, 175 haploinsufficiency, 26 definition, 80 implicit experiment and determination of, gene knockout, 196 17–20 in laboratory selection assays, 162 incomplete (partial) dominance, 19 lac operon genes, 146–147, 147f loss of heterozygosity and, 201–202 nonreverting T4 rII mutants, 79–80 mutant allele relationship to wild-type allele, null alleles, 14, 26 20–22, 24–27 De novo mutations, 205 nonsense suppressors, 112 de Vries, Hugo, 9, 15 overdominance, 21–22 Dihybrid cross, 32, 33f in phage crosses, 75 Diploid, 5–6, 8, 72 Dominant disease phenotypes, 199 Direct repetition, 101 Dominant-negative mutation, 26, 27 Disease, inferring human gene function from Dosage suppression, 122–123 alleles, 195–206 Double crossovers, 37 complex disease phenotypes, Double helix, DNA, 88, 89f 203–205 Double mutant analysis simple Mendelian disease phenotypes, in metabolic pathways, 50–52, 51f, 57 195–202 in regulatory and signal transduction DNA pathways, 55–56, 56f, 57 replication, 88, 157 as test of epistasis, 57 structure, 88, 89f Downstream, 48, 139 transcription, 89–91, 90f Down syndrome, 204 dnaB, 118–119 Drosophila melanogaster, genome of, 169 DNA polymerase, 153 Dulbecco, Renato, 73 DNA polymorphisms, 10, 11, 38–42, 39f–41f, 44, Duplication 187, 190. See also Polymorphisms gene, 27, 171–172, 202 as genetic markers, 13 whole-genome, 173 © 2015 Cold Spring Harbor Laboratory Press. All rights reserved. This is a free sample of content from Decoding the Language of Genetics. Click here for more information or to buy the book. 214 INDEX E FBI Combined DNA Index System (CODIS), E. coli 11–12 as prototroph, 48 Feedback inhibition, 61, 66 genome size, 169 allosteric interactions, 63–64 human protein production in, 157–159 example, 64–65, 65f induction-repression mechanisms in, 67 in tryptophan biosynthesis, 62–63 Edgar, Robert S., 52–53, 57 speed and reversibility of, 67 Effect size, 191 usage of term, 63 Eisen, Michael, 170, 179 Feldman, Marc, 170, 179 Elongation, 154 Fibrin, 163–165 End-product inhibition, 62–65, 65f, 66, 67 Fibronectin finger domain, t-PA, Energy, 47 164–165, 164f Englesberg, Ellis, 148, 152 Fimbrin, 122, 134 Enhancers, 151, 157 Fine-structure mapping, bacteriophage T4, Enzymes, 47–51 78–80 metabolic regulation at level of enzyme Fisher, Ronald, 43, 46, 133 activity, 62–65 Fitch, Walter, 172, 179 0 0 metabolic regulation at level of enzyme 5 untranslated region (5 UTR), 176, 177 synthesis, 65–67 Flagella, 125–126 Epidermal growth factor domain, t-PA, 164–165, FlyBase, 167 164f Fly room at Columbia University, 32, 46 Epigenetics, 208 Fragile X syndrome, 199 Epistasis, 57, 133 Frameshift mutations, 96–97, 112–115, 175 Eugenic laws, 183 Friedreich’s ataxia, 199 Evolution, 1, 4 Function, 5, 6 as compromise, 163 Functional gene consequences of genome architecture, complementation and definition of, 27–29 160–163 definition, 81–83, 84 conservation of functional sequences, DNA polymorphisms and, 13 167–169 evolutionary conservation of sequences, domain architecture of proteins and their 170–174 genes, 163–166, 164f locus reconciled with, 80–81 duplication and divergence of genes, 171–172 Functional sequences, evolutionary neutral theory of molecular evolution, conservation of, 167–179 170–171 Functional suppression, 117–128 phenotypic