Introduction to Bioorganic Chemistry and Chemical Biology

__Introduction to Bioorganic Chemistry and Chemical Biology__ is the first textbook to blend modern tools of organic chemistry with concepts of biology, physiology, and medicine. With a focus on human cell biology and a problems-driven approach, the text explains the combinatorial architecture of biooligomers (genes, DNA, RNA, proteins, glycans, lipids, and terpenes) as the molecular engine for life. Accentuated by rich illustrations and mechanistic arrow pushing, organic chemistry is used to illuminate the central dogma of molecular biology. __Introduction to Bioorganic Chemistry and Chemical Biology__ is appropriate for advanced undergraduate and graduate students in chemistry and molecular biology, as well as those going into medicine and pharmaceutical science. Copyright page 5 Preface 6 Acknowledgments 8 Dedication 9 Contents 10 Detailed Contents 11 Chapter 1 The Fundamentals of Chemical Biology 20 Why organize a book on chemical biology around biooligomers? 20 1.1 The central dogma of molecular biology 21 The central dogma of molecular biology is an organizing principle for chemical biology 21 1.2 Genes 22 A gene is made up of a promoter and a transcribed sequence 22 1.3 Genomes 24 We have sequenced the human genome and many others. Now what? 24 We are far from understanding cells that we understand the best—Escherichia coli 24 We are even farther from understanding human cells 25 You cannot judge a cell by its genome 27 The observable phenotype belies the hidden genotype 28 1.4 Sources of diversity beyond genomes 28 The transcriptome is the collection of all of the RNA transcripts in a cell 28 RNA splicing amplifies the diversity of the transcriptome 29 Post-translational modification of proteins amplifies the diversity of the proteome 29 Beyond template-directed synthesis of biooligomers 30 1.5 Combinatorial assembly generates diversity 31 Combinatorial assembly of linear biooligomers can generate massive diversity 31 Combinatorial synthesis can be used to synthesize DNA libraries 32 Modular architecture lends itself to the synthesis of non-natural chemical libraries 32 The human immune system uses combinatorial biosynthesis 33 1.6 Some common tools of chemical biology 34 Chromophores reveal invisible molecules 34 Assays connect molecular entities to readily visible phenomena 35 Powerful microbiological screens reveal interesting chemical phenomena 36 Viruses deliver genes efficiently 37 Vast libraries of proteins can be screened in vitro using bacteriophages 38 In vitro screens of DNA and RNA push the limits of library diversity 38 Small molecules take control 38 Short RNA molecules silence gene expression 40 Monoclonal antibodies bind specifically 40 Immortal cancer cell lines serve as mimics of human organs 40 Human stem cells are highly valuable tools for research and medicine 41 Model organisms teach us about humans 41 1.7 Summary 43 Problems 44 Chapter 2 The Chemical Origins of Biology 46 2.1 Mechanistic arrow-pushing is an expression of molecular orbital theory 46 Three properties control chemical reactivity 46 Perturbational molecular orbital theory connects arrow-pushing with quantum mechanics 47 Six canonical frontier orbitals can be used to predict reactivity 48 Electronegativity affects both frontier orbitals and Coulombic interactions 50 Curved mechanistic arrows depict the interaction of filled orbitals with unfilled orbitals 51 There are three basic rules for mechanistic arrow-pushing 51 2.2 Hydrogen bonds and proton transfers 52 Hydrogen bonds involve three atoms 52 Proton transfers to and from heteroatoms are usually very fast 53 Linear geometries are preferred for proton transfers 54 2.3 Prebiotic chemistry 55 HCN and CH2O are key ingredients in the primordial soup 55 Solutions of HCN contain both nucleophile and electrophile at pH 9.2 56 HCN forms purines and pyrimidines under prebiotic conditions 57 Aldol reactions with formaldehyde generate carbohydrates 59 Cyanide catalyzes the benzoin reaction 59 Did we arise from a primordial RNA world? 60 Amino acids arise spontaneously under prebiotic conditions 60 2.4 Nonbonding interactions 61 Essentially everything taking place in the cell involves nonbonding interactions 61 The weak energies of nonbonding interactions are not easily calculated using perturbational molecular orbital theory 62 For nonbonding interactions, the energies can be fitted to a simplified equation 62 van der Waals interactions can be described by the Lennard-Jones potential 63 It is helpful to distinguish reversible from irreversible interactions 64 Entropy makes it difficult to identify favorable states among seemingly endless possibilities 66 The hydrophobic effect results from a balance between attractive forces and entropy 66 2.5 The power of modular design 67 Modular design underlies the five basic types of biooligomers 67 Lability correlates inversely with information longevity 68 Why are esters more reactive than amides? 69 Why are phosphate esters less reactive than carboxylic esters? 70 2.6 Summary 72 Problems 73 Chapter 3 DNA 76 3.1 Forms of DNA 76 The canonical double helix is one of several forms of DNA 76 The organization of genomic DNA molecules depends on the type of organism 77 3.2 The ribonucleotide subunits of DNA 78 Nucleotides are phosphate esters 78 DNA and RNA are polymers of nucleotides 79 Are the heterocyclic DNA bases aromatic? 79 Nucleic acids are not acidic, and DNA bases are not basic 80 The missing 2ʹ-hydroxyl group of DNA confers stability to phosphodiester hydrolysis 81 Modifications to DNA bases are as important as the nucleotide DNA sequence 82 3.3 Elementary forces in DNA 83 Base pairing knits together the two strands of DNA 83 Some non-natural, isomeric bases form effective base pairs 85 Hydrogen bonds are not absolutely essential for complementary base pairing 86 Hoogsteen base pairing is present in triplex DNA 87 Aromatic π stacking stabilizes the DNA double helix 87 Intercalation between DNA base pairs involves π stacking 88 Double-stranded DNA undergoes reversible unfolding and refolding 88 Complementarity drives self-assembly of DNA 90 Short stretches of DNA can fold into hairpins 91 3.4 DNA superstructure 92 Double-stranded DNA forms supercoils 92 Topoisomerases resolve topological problems with DNA 92 Bacterial plasmids are rings of DNA 93 Plasmids contain genes that confer advantageous traits 94 Eukaryotic DNA is coiled around histone proteins 95 3.5 The biological synthesis of DNA by polymerase enzymes 97 DNA polymerases lengthen existing strands 97 DNA polymerases copy with high fidelity 98 Reverse transcriptase lengthens existing DNA strands on an RNA template 98 DNA polymerase incorporates modified thymidylate residues 99 The polymerase chain reaction amplifies DNA through iterative doubling 100 3.6 The chemical synthesis of DNA 101 The race to crack the genetic code drove the development of DNA synthesis 101 The Khorana method of DNA synthesis relies on phosphate coupling chemistry 102 Letsinger recognized the speed and efficiency of phosphite couplings 102 Caruthers synthesized DNA by using phosphoramidites on solid phase 103 Automated oligonucleotide synthesis is performed on glass particles 104 Modern automated DNA synthesis involves repetitive four-step cycles 105 The 4,4ʹ-dimethoxytrityl group is deprotected through an SN1 reaction 105 Tetrazole serves as an acid catalyst in phosphoramidite couplings 106 Capping unreacted 5ʹ-hydroxyl groups prevents the propagation of mistakes 106 Oxidation of unstable phosphites generates stable phosphates 107 Aqueous ammonium hydroxide cleaves and deprotects synthetic DNA 108 Microarrays of DNA facilitate screening 108 Why are DNA and RNA made up of five-membered ring sugars? 109 3.7 Separation of DNA molecules by electrophoresis 110 Scientists use different criteria for the purity of biological macromolecules versus small, organic molecules 110 Agarose gel is used for electrophoresis of long DNA molecules 111 Capillary electrophoresis is used for analytical separation of short DNA molecules 113 DNA dideoxy sequencing capitalizes on the tolerance of DNA polymerase 114 Large-scale sequencing methods avoid the need for electrophoresis 115 3.8 Recombinant DNA technology 116 Molecular biology connects DNA molecules to biological phenotypes 116 Restriction endonucleases cut DNA at specific sites and facilitate re-ligation 117 Mutations in DNA can lead to changes in expressed proteins 120 Site-directed mutagenesis involves labile plasmid templates 121 3.9 Nucleic acid photochemistry 121 Ultraviolet radiation promotes [2+2] photodimerization of thymine and uracil bases 121 Thymine dimers in DNA can be repaired 122 Psoralens intercalate between DNA base pairs and photocrosslink opposing strands 123 3.10 DNA as a target for cytotoxic drugs 124 Cell division is highly controlled in normal human cells 124 Dividing human cells must pass through checkpoints, or die 124 Traditional chemotherapy targets DNA in rapidly dividing cells, cancerous or not 125 Inhibition of thymine biosynthesis triggers apoptosis during the S phase of the cell cycle 126 Adding the methyl group to thymine is essential for DNA synthesis 127 DNA is a nucleophile 129 Simple alkylating agents are highly mutagenic 129 Bifunctional alkylating agents that crosslink DNA are highly cytotoxic 130 Strained rings can bring highly reactive functional groups to DNA 131 Epoxide alkylators of DNA are highly mutagenic 132 Aziridinium rings are relatively selective alkylators of DNA 133 Cyclopropane rings can serve as spring-loaded electrophiles 134 Free radicals and oxygen conspire to cleave DNA sugars 136 Enediyne antitumor antibiotics cleave both strands of DNA via para-benzyne diradicals 137 Some highly reactive enediyne natural products are protected by protein delivery vehicles 141 Bleomycin catalyzes the formation of reactive oxygen species 142 3.11 Summary 143 Problems 144 Chapter 4 RNA 150 4.1 RNA structure 151 The nucleotide subunits of RNA are subtly different from those of DNA 151 The 2ʹ-OH of RNA confers high chemical reactivity 151 Ubiquitous ribonucleases rapidly degrade RNA 152 The 5-methyl group of thymine is a form of chemical ID 153 RNA adopts globular shapes because it is single-stranded 154 4.2 RNA synthesis 158 RNA polymerases create new strands of RNA 158 DNA primase is just another RNA polymerase 159 4.3 Transcriptional control 160 DNA sequences determine start sites and stop sites for RNA polymerase 160 Transcription factors bind to DNA with exquisite sequence specificity 161 Transcription can be controlled by small molecules 162 Transcription of mRNA in human cells involves many proteins and many regions of DNA 164 The yeast two-hybrid system provides a transcription-based tool to identify protein–protein interactions 165 4.4 mRNA processing in eukaryotes 167 After synthesis, eukaryotic organisms modify their mRNA extensively 167 The ends of the mRNA are capped and polyadenylated 168 Most eukaryotic genes require mRNA splicing 169 Some RNA introns undergo self-splicing without a spliceosome 170 4.5 Controlled degradation of RNA 171 Ribonuclease H degrades RNA•DNA duplexes 171 RNA-induced silencing complexes target specific mRNA sequences 172 RNA interference is a useful laboratory tool 174 4.6 Ribosomal translation of mRNA into protein 175 The ribosome catalyzes oligomerization of α-amino esters 175 The ribosome is a massive molecular machine, half protein and half RNA 176 tRNA molecules are heavily processed and adopt fixed shapes 178 The genetic code allows one to translate from mRNA sequence into protein sequence 180 tRNA synthetases recognize amino acids and nucleotides 181 What controls the beginning and end of translation? 182 Translational initiation is a focal point for control of protein synthesis 184 A protein escorts each aminoacyl-tRNA to the ribosome for fidelity testing 185 The genetic code can be expanded beyond 20 amino acids 186 Ligand-dependent riboswitches control protein expression 188 Many antibiotics target bacterial protein synthesis 189 4.7 From oligonucleotide libraries to protein libraries 190 Automated oligonucleotide synthesis facilitates generation of both DNA and RNA oligonucleotide libraries 190 RNA libraries can be screened for ribozymes 192 mRNA libraries can be expressed as protein libraries 193 4.8 Summary 194 Problems 195 Chapter 5 Peptide and Protein Structure 198 5.1 Amino acids and peptides 199 The standard ribosomal amino acids include a broad range of functionalities 199 Amino acids are polymerized into peptides and proteins 200 Amino acid side chains have predictable protonation states 202 Amino acid side chains mediate protein–protein interactions 203 5.2 Solid-phase peptide synthesis 204 Peptides can be used as pharmaceuticals 204 Excess reagents and optimized chemistry allow high-throughput peptide synthesis 206 Chemical peptide synthesis involves repeated additions of activated carboxylates to the N terminus 207 The need to remove excess reagents and chemical by-products drove the development of solid-phase peptide synthesis 207 Either acid- or base-labile carbamates are used for the temporary protection of the Nα group 208 Carbodiimides drive condensation to form peptide bonds 209 Side reactions can compete with peptide coupling reactions 209 HOBt minimizes side reactions in carbodiimide couplings 210 Uronium coupling agents provide even faster amide bond formation 211 Resins for solid-phase peptide synthesis are made of plastic 212 Cleavable linkers between the synthesized peptide and solid support provide stable, yet reversible, attachments 212 Side-chain protecting groups come off under acidic conditions 214 Peptide nucleic acids lack phosphate esters and ribofuranose rings 215 Native chemical ligation generates cysteinyl amides through aminolysis of thiol esters 216 5.3 Fundamental forces that control protein secondary structure 218 Secondary structure involves different patterns of hydrogen bonding between backbone amides 218 α Helices allow effective hydrogen bonding between neighboring amide N–H and C=O 219 β Sheets satisfy hydrogen bonding by backbone amides with linkages between different strands 220 Turn structures have minimal hydrogen bonding between backbone amides 221 Rotation about substituted ethanes, butanes, and pentanes reveals the fundamental forces dictating protein folding 222 Stereoelectronic effects distinguish amides and esters from substituted ethenes 223 Interactions between allylic substituents and alkene substituents limit the conformation of substituted propenes 224 Allylic strain explains the dominance of two types of secondary structures 225 5.4 The chemistry of disulfide crosslinks 226 Cystine disulfides form readily under oxidative conditions 226 Glutathione is an intracellular thiol buffer 226 Cystine disulfides in proteins are in equilibrium with glutathione disulfides 227 Combinatorial crosslinking and protein misfolding can complicate attempts to produce disulfide-containing proteins 228 Concentrations of glutathione depend on location 229 5.5 Protein domains have structural and functional roles 229 Biological protein assemblies exhibit hierarchical structures 229 The tertiary and quaternary structures of proteins access a wide range of different archetypal protein folds 230 Zinc-finger domains recognize DNA sequences 231 A number of common domains are based on β-sandwich architectures 232 Calcium promotes interactions between cadherin domains 234 WD domains fit together like triangular slices of a cake 235 Collagen is formed from a three-stranded helix 235 Protein kinase domains and seven-transmembrane domains have key roles in signal transduction 236 The RNA recognition motif domain binds to single-stranded RNA 237 Peptide-binding domains can confer modular functions to proteins 237 5.6 Higher levels of protein structure 238 The tertiary structure consists of one or more domains 238 Quaternary structure consists of highly integrated assemblies of independent, folded proteins 239 5.7 summary 240 Problems 242 Chapter 6 Protein Function 248 6.1 Receptor–ligand interactions 248 The thermodynamics and kinetics of receptor–ligand interactions govern all processes in biology 248 Dose–response curves measure protein function, and correlate with affinity 251 Highly specific protein–small-molecule interactions are useful 253 6.2 A quantitative view of enzyme function 255 Enzymes are catalytic receptors 255 Measurements of enzyme efficiency must account for substrate binding and catalysis 257 6.3 A mechanistic view of enzymes that catalyze multistep reactions 259 Protein kinases and proteases catalyze reactions through multistep mechanisms 259 Protein kinases share a common motif 260 Regulation of protein kinase activity requires allosteric binding 263 Phosphorylation can also activate kinases 265 Proteases serve roles in degradation and protein signaling 266 Cysteine proteases catalyze amide hydrolysis by using a nucleophilic cysteine thiolate 269 Enzymes proceed via mechanisms with the minimum number of different types of transition states 270 Serine proteases cleave amides by using an alkoxide nucleophile 271 Metalloproteases use Zn2+ ions to activate the nucleophilic water and stabilize the tetrahedral intermediate 272 Activation can control protease activity 273 Reversible enzyme inhibitors include transition-state analogs with very high affinity 274 Mechanism-based enzyme inhibitors react with residues at the active site 277 Cooperative binding requires careful placement of functional groups 279 Triosephosphate isomerase is nearly a perfect enzyme 281 6.4 Enzymes that use organic cofactors 282 Enzyme cofactors extend the capabilities of enzymes 282 Thiamine pyrophosphate provides a stabilized ylide 283 The dihydropyridine group of niacin (vitamin B3) provides a reactive hydride 284 The pyridoxal cofactor serves as an electron sink 285 6.5 Engineering improved protein function 288 Protein engineering provides power tools for the dissection of protein function and the development of hyperfunctional molecules 288 Alanine scanning assigns function to side chains and motifs 288 Alanine scanning allows reverse engineering of protein function 289 Protein engineering enables improvement of protein function 291 Protein engineering enables a change of protein function 292 Most random mutations debilitate rather than enhance protein function 293 Recombination generates new combinations of existing mutations 293 Screens work well for modest numbers of protein variants, but exceptionally diverse libraries require selections 294 6.6 Summary 294 Problems 296 Chapter 7 Glycobiology 300 7.1 Structure 300 There are 10 common monosaccharide building blocks for human glycans 300 Glycobiology uses a compact form of nomenclature 302 Polar effects and stereoelectronic effects determine the relative stability of α and β anomers 303 7.2 The chemistry and enzymology of the glycosidic bond 305 Monosaccharide carbonyl groups form hemiacetals 305 Six- and five-membered ring hemiacetals are common 305 Chemical hydrolysis of glycosidic bonds involves SN1 reactions 308 Enzymatic hydrolysis of glycosidic bonds involves SN1-like SN2 reactions 309 Members of all classes of glycosylhydrolases have two carboxylic acids in the active site 309 Substrate distortion is important in glycosylhydrolase enzymes 310 Inhibiting glycosylhydrolase enzymes fight influenza 312 Glycosyltransferases transfer monosaccharides from glycosyl phosphate donors 313 Glycosyltransferases transfer glycosyl groups from phosphates 313 7.3 Polysaccharides 315 Diastereomers of glucose polymers have very different properties 315 Chitin is a resilient polymer in insect cuticles 316 Some tissues are cushioned by the polysaccharide hyaluronan 317 Meningococci are coated with polysialic acids like those found on neurons 317 7.4 Glycoproteins 318 Glycosylation of human proteins occurs in the vesicles of the secretory pathway 318 Synthesis of O-linked glycoproteins begins with the addition of xylose or N-acetylgalactose 319 O-linked proteoglycans are polyanions 320 The carbohydrate moiety of N-linked glycoproteins is initially added as an oligosaccharide 322 An Asn-Xxx-Ser motif adopts a reactive conformation in the N-glycosylation of proteins 323 The processing of glycans occurs during vesicular trafficking 324 A few human proteins are C-mannosylated on tryptophan residues 327 Glycosylation of proteins sometimes, but not always, affects the intrinsic function of the protein 327 Most extracellular signaling proteins are glycosylated with oligosaccharides 328 Many protein pharmaceuticals are glycosylated 329 Cell–cell recognition is often mediated by glycoproteins 330 Introduction of N-glycosylation sites can improve protein pharmaceuticals 331 Modified sugars can carry reactive groups through the glycoprotein biosynthesis pathway 331 7.5 Glycolipids 333 Glycosphingolipids are lipid-like glycoconjugates 333 Glycosylphosphatidylinositols from pathogens are potential vaccines 334 7.6 Glycosylation in the cytosol 335 O-glycosylation of proteins in the cytosol with β-GlcNAc is analogous to phosphorylation 335 Drugs are targeted for export by glucuronidation 337 7.7 Chemical synthesis of oligosaccharides 337 Anomeric stereochemistry is controlled by the anomeric leaving group and the 2 substituent 337 Modern oligosaccharide synthesis takes advantage of activatable leaving groups 339 Synthesis of oligosaccharides still requires a skilled synthetic organic chemist 340 7.8 Proteins that bind to carbohydrate ligands 341 Glycans differentiate the surfaces of human cells 341 Most carbohydrate-binding proteins are multivalent 341 Human lectins mediate selective adhesion of leukocytes 345 Human blood group antigens are found on glycolipids and glycoproteins 345 Some toxins enter cells through multivalent carbohydrate recognition 346 Microarray technology facilitates the analysis of protein–glycan interactions 347 7.9 Glucose homeostasis and diabetes 349 Human metabolism and paper-burning are related transformations 349 Glucose reacts with proteins over time 350 Glucose-derived protein crosslinks are not necessarily permanent 351 There is a big market for artificial ligands for human taste receptors 352 7.10 Summary 354 Problems 356 Chapter 8 Polyketides and Terpenes 358 8.1 The Claisen reaction in polyketide biosynthesis 359 The diverse structures of polyketide natural products belie their iterative construction 359 Polyketides are derived from two-carbon and three-carbon building blocks 359 8.2 The biosynthesis of fatty acids is a paradigm for polyketide biosynthesis 361 Fatty acids have varying levels of unsaturation 361 Fatty acid/polyketide synthases are categorized on the basis of their supramolecular structure 362 The acyl carrier protein shuttles the growing polyketide chain from one catalytic domain to another 363 A transacylase loads monomeric subunits onto the carrier protein 363 Ketosynthases catalyze a decarboxylative Claisen condensation 364 Ketoreductases catalyze hydride transfer from NADPH 364 Dehydratases catalyze β-elimination 365 Enoyl reductases catalyze a conjugate reduction 365 A thioesterase uses a catalytic triad to cleave the acyl group from the acyl carrier protein 366 Enzymes associated with the endoplasmic reticulum put the finishing touches on fatty acids 367 8.3 The biological role of human polyketides 367 Eight categories of lipids are found in biology 367 Lipid membranes are composed of lipids with a polar head group and a nonpolar tail 367 The lipid bilayer entropically favors interactions between embedded molecules 369 Phospholipases generate distinct chemical signals by hydrolyzing various bonds of phospholipids 369 Phospholipase Cβ generates two signaling molecules 370 Arachidonic acids are converted into diverse signaling molecules during inflammation 371 Sphingosine derivatives are important in intracellular signaling 374 Metal-catalyzed hydrogenation of unsaturated fats changed the human diet 376 Some lipids from lower organisms contain cyclopropane rings 377 Acylation of human proteins induces membrane localization 378 Chemical transformation of fats generates useful compounds 380 8.4 Nonhuman polyketide natural products 381 Several tricks amplify the potential diversity of polyketide natural products 381 Streptomyces has mastered polyketide biosynthesis 383 The modular genetic organization of type I polyketide synthases facilitates genetic reprogramming 385 Sometimes additional methyl groups are added to the polyketide backbone 388 8.5 Nonribosomal peptide synthases 388 Ribosomal translation is suited to the production of large proteins, not short peptides 388 Most bioactive peptide secondary metabolites are generated by peptide synthases, not by ribosomes 389 8.6 Human terpenes 390 Early chemists recognized terpenes as oligomers of isoprene 390 Cationic additions lead to linear chains 391 Prenyl subunits arise through enolate chemistry 392 Inhibition of terpene biosynthesis is the number one treatment for heart disease 394 Prenylated quinones serve important roles in redox chemistry 396 Prenylation of proteins confers membrane affinity 398 Tail-to-tail coupling of terpenyl diphosphates generates precursors of higher-order terpenes 399 Polyene cyclizations generate many rings in a single reaction 400 Humans lack genes for retinoid biosynthesis 402 8.7 Nonhuman terpene natural products 404 Plants and microorganisms produce a much wider range of terpene natural products than humans 404 Isomerization of geranyl diphosphate to linalyl diphosphate facilitates cyclization 405 The 2-norbornyl cation exhibits exceptional behavior 407 Minor products offer clues to the enzymatic mechanisms of terpene cyclases 408 Some terpene cyclases generate medium-sized rings 409 The biosynthesis of some terpenes involves nontraditional [1,3] hydride shifts 410 Plants can also make complex triterpenes from squalene 410 Hyperthermophilic archaebacteria produce cyclic lipids from terpenes 411 8.8 Summary 412 Problems 413 Chapter 9 Chemical Control of Signal Transduction 416 9.1 Signal transduction 418 Chemical signaling is universal 418 The field of biology is full of cryptic acronyms and ambiguous symbols 418 Fast cellular responses do not involve the production of proteins 420 Cell contraction and vesicle fusion: fast calcium-dependent responses that do not involve changes in transcription 421 Cell signaling can involve pathways within cells and/or between cells 422 9.2 An overview of signal transduction pathways in human cells 423 There are seven major signal transduction pathways in humans 423 Chemical genetics involves the use of small molecules to understand gene function 424 Screening identifies small molecules for use in chemical genetics 425 9.3 Nuclear receptors 426 Binding of small-molecule ligands activates nuclear receptor transcription factors 426 Some nuclear receptors translocate from cytoplasm to the nucleus, and bind DNA as homodimers 428 Some nuclear receptors are localized in the nucleus and bind to DNA as heterodimers 428 The mode of nuclear receptor dimerization determines DNA sequence selectivity 429 Human cells can be rewired for control by Drosophila nuclear receptors 430 Steroids make highly potent pharmaceuticals 431 Nonsteroidal ligands for nuclear receptors are also widely used as drugs 432 Drugs can be designed to target specific mutations of nuclear receptors 433 9.4 Cell-surface receptors that interact directly with transcription factors 434 Hematopoietic proliferation and differentiation are controlled by molecular signals 434 Human cytokines can be used as pharmaceuticals 435 The JAK–STAT pathway involves a receptor, a kinase, and a transcription factor 436 Small-molecule dimerizers can be used to demonstrate functional relationships between proteins 437 Other interferons bind to heterodimeric and higher-order receptor assemblies 438 Synthetic N-hydroxysuccinimidyl esters can acylate proteins in aqueous solution 438 Transforming growth factor-β receptors possess built-in serine/threonine kinase domains 440 9.5 Receptor tyrosine kinases 440 Receptor tyrosine kinases control tissue growth 440 Growth factors have a role in proliferation of urothelial cells 441 Comparing receptor tyrosine kinases and cytokine receptors reveals useful commonalities 442 The ATP-binding sites of receptor tyrosine kinases are sufficiently different that they can be selectively inhibited by small molecules 443 Transphosphorylation of tyrosine residues is sequential 443 Receptor tyrosine kinases signal growth via a MAP kinase cascade 444 Many signal transduction pathways involve abundant small molecules and scarce proteins 445 Receptor tyrosine kinases turn on calcium signaling pathways via phospholipase C 447 Receptor tyrosine kinases broadcast both proliferative and anti-apoptotic signals via Akt 448 The differences between various receptor tyrosine kinase pathways are less important than the similarities 449 Chemical methods for isolation and identification of kinase substrates 449 9.6 G protein-coupled receptors 450 Seven-transmembrane domain G protein-coupled receptors can respond to a wide range of ligands with high dynamic range 450 High-affinity ligand–receptor interactions lead to slow response times and low dynamic range 451 G proteins allow low-affinity receptors to have high sensitivity 452 Seven-transmembrane domain G protein-coupled receptors can respond to a wide range of ligands with high dynamic range 453 Heterotrimeric G proteins are designed to generate divergent signals 453 Some elements of signal transduction pathways can integrate inputs 453 Contraction of endothelial smooth muscle is controlled by Gαq 455 Some bacterial toxins reprogram Gα subunits, with deadly results 456 Adenylyl cyclase and phospholipase Cβ are the most common mediators of 7TM GPCRs 457 Many pharmaceuticals act on 7TM GPCRs that respond to ligands derived from amino acids 457 Opioids act on 7TM GPCRs that bind to neuropeptides 459 Smell and taste involve 7TM GPCRs 460 How do you bind to a photon? 461 The decision between immortality and destiny involves the protein Wnt and the β-catenin pathway 462 A seven-transmembrane receptor that controls development does not bind to an extracellular ligand 463 9.7 Ion channel receptors 464 Ion channel receptors provide an ultra-fast response to stimuli 464 A human cell is a bag of potassium in a salty ocean 465 Voltage-gated ion channels are activated by transmembrane differences in ion concentrations 466 Pentameric Cys-loop receptors are gated by neurotransmitters 468 The nicotinic acetylcholine receptor is a popular targ