MEDIA AND ASSESSMENT ∞LaunchPad ata.developin conecting dge to real scen ance w All of the new media resources for Biochemistry will be the available in our new system. in the classr oom)and aligned assessment questions www.macmillanhighered.com/launchpad/berg8e for auizzes and exams Newly Updated Clicke LaPad dynamic.fully integrated learnin rings together l of our teaching an students' ce.It ins the full sof Word and orenidentsandins PowerPoint (PPT) Newly Updated Lecture PowerPoints have been NEW Case Studies are a series of biochemistry case studies you can integrate into your course. ed e case study gives students practice in working with ncluding key illu that instructors can adapt to their teaching styles. Updated Layered PPTs dec all and ent comstep-bytp. Updated" xtbook Im es and Tables as high . T to ensure maximum clarity and visibility. The Clinical Co R The L Gregory 0 dent have learned in the book tonove medicalsitu ations.Students read clinical case studies and use basic biochemistry concepts to solve the Hundreds of self-graded practice prob- lems allow students to test their understanding of concepts explained in the text,with immedi ate feedback. The metabolic map helps students under. stand the principles and at oplications of the core metabolic pathways.Students can work through guided tutorials with embedded fAMbyTo-ikec The e side (top)a Jmol tutorials by Jeffrey Cohlberg,California by b es on the side of each of the extracellula State University at long beach.teach students
viii All of the new media resources for Biochemistry will be available in our new system. www.macmillanhighered.com/launchpad/berg8e LaunchPad is a dynamic, fully integrated learning environment that brings together all of our teaching and learning resources in one place. It also contains the fully interactive e-Book and other newly updated resources for students and instructors, including the following: • NEW Case Studies are a series of biochemistry case studies you can integrate into your course. Each case study gives students practice in working with data, developing critical thinking skills, connecting topics, and applying knowledge to real scenarios. We also provide instructional guidance with each case study (with suggestions on how to use the case in the classroom) and aligned assessment questions for quizzes and exams. • Newly Updated Clicker Questions allow instructors to integrate active learning in the classroom and to assess students’ understanding of key concepts during lectures. Available in Microsoft Word and PowerPoint (PPT). • Newly Updated Lecture PowerPoints have been developed to minimize preparation time for new users of the book. These files offer suggested lectures including key illustrations and summaries that instructors can adapt to their teaching styles. • Updated Layered PPTs deconstruct key concepts, sequences, and processes from the textbook images, allowing instructors to present complex ideas step-by-step. • Updated Textbook Images and Tables are offered as high-resolution JPEG files. Each image has been fully optimized to increase type sizes and adjust color saturation. These images have been tested in a large lecture hall to ensure maximum clarity and visibility. • The Clinical Companion, by Gregory Raner, The University of North Carolina at Greensboro and Douglas Root, University of North Texas, applies concepts that students have learned in the book to novel medical situations. Students read clinical case studies and use basic biochemistry concepts to solve the medical mysteries, applying and reinforcing what they learn in lecture and from the book. • Hundreds of self-graded practice problems allow students to test their understanding of concepts explained in the text, with immediate feedback. • The Metabolic Map helps students understand the principles and applications of the core metabolic pathways. Students can work through guided tutorials with embedded assessment questions, or explore the Metabolic Map on their own using the dragging and zooming functionality of the map. • Jmol tutorials by Jeffrey Cohlberg, California State University at Long Beach, teach students MEDIA AND ASSESSMENT Figure 34.3 Recognition of a PAMP by a Toll-like receptor. The structure of TLR3 bound to its PAMP, a fragment of double-stranded RNA, as seen from the side (top) and from above (bottom). Notice that the PAMP induces receptor dimerization by binding the surfaces on the side of each of the extracellular domains. [Drawn from 3CIY.pdb]
how to create models of proteins in Jmol based end-of-chapter questions in the book,giving stu- on data from the Protein Data Bank.By working dents a way to practice applying chapter content in an online environment. stude this i Flashcards are an interactive tool that allows eaTtoue students to study key terms from the book. and function of enzymes LearningCurve is a self-asse ts Living figures allow students to explore protein thei derstan structure in 3-D scanm and rotate th erstanding of mapa the with different display style stick,ribbon,backbone)by means of a user-friendly interface. Updated Student Companion orials by Neil D.Clarke help [1-4641-8803-31 aiti For each chapter of the textbook,the Student Companior cove includes: Chapter Learning Objectives and Summary me ment Probler including multiple proteins choice.short-answer.matching questions,and chal- NEW animations show students biochemical pro- lenge problems,and their answers cesses in motion.The eighth edition includes many ded Solutions to end-of-chapter problems new animations Online end-of-ch stions are assignable ndf-raded ix
ix how to create models of proteins in Jmol based on data from the Protein Data Bank. By working through the tutorial and answering assessment questions at the end of each exercise, students learn to use this important database and fully realize the relationships between the structure and function of enzymes. • Living figures allow students to explore protein structure in 3-D. Students can zoom and rotate the “live” structures to get a better understanding of their three-dimensional nature and can experiment with different display styles (space-filling, ball-andstick, ribbon, backbone) by means of a user-friendly interface. • Concept-based tutorials by Neil D. Clarke help students build an intuitive understanding of some of the more difficult concepts covered in the textbook. • Animated techniques help students grasp experimental techniques used for exploring genes and proteins. • NEW animations show students biochemical processes in motion. The eighth edition includes many new animations. • Online end-of-chapter questions are assignable and self-graded multiple-choice versions of the end-of-chapter questions in the book, giving students a way to practice applying chapter content in an online environment. • Flashcards are an interactive tool that allows students to study key terms from the book. • LearningCurve is a self-assessment tool that helps students evaluate their progress. Students can test their understanding by taking an online multiplechoice quiz provided for each chapter, as well as a general chemistry review. Updated Student Companion [1-4641-8803-3] For each chapter of the textbook, the Student Companion includes: • Chapter Learning Objectives and Summary • Self-Assessment Problems, including multiplechoice, short-answer, matching questions, and challenge problems, and their answers • Expanded Solutions to end-of-chapter problems in the textbook
MOLECULAR EVOLUTION es or other mo r evolutionary insights Only Lamino acids make up proteins(p.29) Glycogen synthase is homologous to glycogen Why this set of 20 amino acids?(p.35) phosphorylase(p.631) Sickle-cell trait and malaria(p.206 A recurring motif in the activation of carboxyl groups (D.649) Additional human globin genes (p.208) Catalytic triads in hydrolytic enzymes(p.258) Prokaryotic counterparts of the ubiquitin pathway and the proteasome(p.686)】 A family of pyridoxal-dependent enzymes(p.692) Evolution of the urea cycle(p.696) P-loop NTPase domains(p.280 The P-loop NTPase domain in nitrogenase(p.716) Conserved catalytic core in protein kinases (p.298) Conserved amino acids in transaminases determine amino Why do different human blood types exist?(p.331) acid chirality(p.721) Feedback inhibition(p.731) Archaeal membranes(p.346) nthesis(p.749) Ion pumps(p.370 Rib P-type ATPases(p.374) Increase in urate levels during primate evolution (p.761) ATP-binding cassettes(p.374) Deinococcus radiodurans illustrates the power of dna repair systems (p.828) DNA polymerases(p.829) Metabolism in the RNA world (p.444) Thymine and the fidelity of the genetic message(p.849) Why is glucose a prominent fuel?(p.451) Sigma factors in bacterial transcription(p.865) NAD*bindings Similarities in transcription between archaea and eukaryotes (p.876) Evolution of glycolysis and gluconeogenesis(p.487) Evolution of spliceosome-catalyzed splicing(p.888) The a-ketoglutarate dehydrogenase complex(p.505) Classes of aminoacyl-tRNA synthetases(p.901) Domains of succinylCoA synthetase(p.507) Composition of the primordial ribosme(p.903) Evolution of the citric acid cycle(p.516) HomologousG proteins(p.908) Mitochondrial evolution(p.525) A family of proteins with common ligand-binding domains Conserved structure of cytochrome(p.541) (p.930) Common features of AT andGproteins(p.548) The independent evolution of DNA-binding sites of regulatory proteins(p.931) PnCP-)ndb Key principles of gene regulation are similar in bacteria and Related uncoupling proteins(p.556) archaea(p.937) Chloroplast evolution(p.568) CpG islands(p.949) Evolutionary originsof photosynthesis(p.584) onse elements(p.955) Evolution of the C4 pathway (p.601) miRNAs in gene evolution (p.957) The odorant-receptor family (p.963 The relationship of the Calv Photoreceptor evolution(p.973) Increasing sophisti cation of glycogen phosphorylase regulation(p.629) eationship of tubulin to prokaryotic proteins(p.1023) ◆
x Only L amino acids make up proteins (p. 29) Why this set of 20 amino acids? (p. 35) Sickle-cell trait and malaria (p. 206) Additional human globin genes (p. 208) Catalytic triads in hydrolytic enzymes (p. 258) Major classes of peptide-cleaving enzymes (p. 260) Common catalytic core in type II restriction enzymes (p. 275) P-loop NTPase domains (p. 280) Conserved catalytic core in protein kinases (p. 298) Why do different human blood types exist? (p. 331) Archaeal membranes (p. 346) Ion pumps (p. 370) P-type ATPases (p. 374) ATP-binding cassettes (p. 374) Sequence comparisons of Na1 and Ca21 channels (p. 382) Small G proteins (p. 414) Metabolism in the RNA world (p. 444) Why is glucose a prominent fuel? (p. 451) NAD1 binding sites in dehydrogenases (p. 465) Isozymic forms of lactate dehydrogenase (p. 487) Evolution of glycolysis and gluconeogenesis (p. 487) The a-ketoglutarate dehydrogenase complex (p. 505) Domains of succinyl CoA synthetase (p. 507) Evolution of the citric acid cycle (p. 516) Mitochondrial evolution (p. 525) Conserved structure of cytochrome c (p. 541) Common features of ATP synthase and G proteins (p. 548) Pigs lack uncoupling protein 1 (UCP-1) and brown fat (p. 556) Related uncoupling proteins (p. 556) Chloroplast evolution (p. 568) Evolutionary origins of photosynthesis (p. 584) Evolution of the C4 pathway (p. 601) The relationship of the Calvin cycle and the pentose phosphate pathway (p. 610) Increasing sophistication of glycogen phosphorylase regulation (p. 629) Glycogen synthase is homologous to glycogen phosphorylase (p. 631) A recurring motif in the activation of carboxyl groups (p. 649) Prokaryotic counterparts of the ubiquitin pathway and the proteasome (p. 686) A family of pyridoxal-dependent enzymes (p. 692) Evolution of the urea cycle (p. 696) The P-loop NTPase domain in nitrogenase (p. 716) Conserved amino acids in transaminases determine amino acid chirality (p. 721) Feedback inhibition (p. 731) Recurring steps in purine ring synthesis (p. 749) Ribonucleotide reductases (p. 755) Increase in urate levels during primate evolution (p. 761) Deinococcus radiodurans illustrates the power of DNA repair systems (p. 828) DNA polymerases (p. 829) Thymine and the fidelity of the genetic message (p. 849) Sigma factors in bacterial transcription (p. 865) Similarities in transcription between archaea and eukaryotes (p. 876) Evolution of spliceosome-catalyzed splicing (p. 888) Classes of aminoacyl-tRNA synthetases (p. 901) Composition of the primordial ribosome (p. 903) Homologous G proteins (p. 908) A family of proteins with common ligand-binding domains (p. 930) The independent evolution of DNA-binding sites of regulatory proteins (p. 931) Key principles of gene regulation are similar in bacteria and archaea (p. 937) CpG islands (p. 949) Iron-response elements (p. 955) miRNAs in gene evolution (p. 957) The odorant-receptor family (p. 963) Photoreceptor evolution (p. 973) The immunoglobulin fold (p. 988) Relationship of tubulin to prokaryotic proteins (p. 1023) This icon signals the start of the many discussions that highlight protein commonalities or other molecular evolutionary insights. MOLECULAR EVOLUTION
CLINICAL APPLICATIONS sthe sar ofi thetextdtiobrieer clinical correlations appear in the text as appropriate. Osteogenesis imperfecta(p.6) Triose phosphate isomerase deficiency (p.454) Protein-misfolding(.56 Excessive fructose cons mption(p.66) Protein modification and scurvy(p.57) Lactose intolerance (p.467) Antigen/antibody detection with ELISA(p.82) Galactosemia(p.468) Synthetic peptides asdrugs(p.92) Aerobic olycolysis and cancer (p 474) PCR in diagnostics and forensics (p.142) sedeficiency(p.512) Gene therapy (p.164) Aptamers in biotechnology and medicine(p.187) Functional magnetic resonance i imaging(p.193) Beriberi and mercury poisoning(p.515) 2.3-BPG and fetal hemoglobin (p.201) Frataxin mutations cause Friedreich's ataxia(p.531) Carbon monoxide poisoning (p.201) species(ROS)are implicated inavariety Sickle-cell anemia(p.205) Thalassemia(p.207) ROS may be mportant in signal transduction(p.540) Aldehyde dehydrogenase deficiency(p.228) IF1overexpression and cancer(p.554) Brown adipose tissue(p.555) Action of penicillin (p.239) Protease inhibitors (p.263) Mild uncouplers sought as drugs(p.557) Carbonic anhydrase Mitochondrial diseases(p.557) Isozymes as a sign of tissue damage (p.293) Trypsin inhibitor helps prevent pancreatic damage(p.302) Gluc Emphysema(p.303) p.303) ing involv ade of zymogen activations Developing drugs for type 2 diabetes (p.636) Vitamin K(p.306) Glycogen-storage diseases(p.637) Chanarin-Dorfman syndrome(.648) Antithrombin and hemorrhage (p.307) Carnitine deficiency (p.650) Hemophilia(p.308) Zellweger syndrome (p.657 Monitoring change glycosylated hemoglobin(p.321) Diabetic ketosis(p.659) Erythropoietin(p.327 Ketogenic diets to treat epilepsy (p.660) Hurler disease(p.327) Mucins(p.329) p.661 acids may contribute to pathological conditions Blood g groups(p.331) I-cell disease(p.332) Influenza virus binding(p.335) Effects of aspirin on signaling pathways(p.669) Clinical applications of lipo es(p.349) Diseases resulting from defects in transporters of amino Aspirin and ibuprofen (p.353) acids(p.682) Diseases resulting from defects in E3 proteins(p.685) Digitalis and congestive heart failure(p.373) Multidrug resistance (p 374) Drugs target the ubiquitin-proteasome system(p.687) Long OT syndrome(p.388) Using pro tuberculosis(p.687) Signal-transduction pathways and cancer (p.416) Monoclonal antibodies as anticancer drugs(p.416) Inherited defects of the urea cycle(hyperammonemia) Protein kinase inhibitors as anticancer drugs(p.417) (p.697) G-proteins,cholera and whooping cough(p.417) Alcaptonuria,maple syrup urine disease,and Vitamins(p.438) phenylketonuria (p.705)
xi Osteogenesis imperfecta (p. 46) Protein-misfolding diseases (p. 56) Protein modification and scurvy (p. 57) Antigen/antibody detection with ELISA (p. 82) Synthetic peptides as drugs (p. 92) PCR in diagnostics and forensics (p.142) Gene therapy (p. 164) Aptamers in biotechnology and medicine (p. 187) Functional magnetic resonance imaging (p. 193) 2,3-BPG and fetal hemoglobin (p. 201) Carbon monoxide poisoning (p. 201) Sickle-cell anemia (p. 205) Thalassemia (p. 207) Aldehyde dehydrogenase deficiency (p. 228) Action of penicillin (p. 239) Protease inhibitors (p. 263) Carbonic anhydrase and osteopetrosis (p. 264) Isozymes as a sign of tissue damage (p. 293) Trypsin inhibitor helps prevent pancreatic damage (p. 302) Emphysema (p. 303) Blood clotting involves a cascade of zymogen activations (p. 303) Vitamin K (p. 306) Antithrombin and hemorrhage (p. 307) Hemophilia (p.308) Monitoring changes in glycosylated hemoglobin (p. 321) Erythropoietin (p. 327) Hurler disease (p. 327) Mucins (p. 329) Blood groups (p. 331) I-cell disease (p. 332) Influenza virus binding (p. 335) Clinical applications of liposomes (p. 349) Aspirin and ibuprofen (p. 353) Digitalis and congestive heart failure (p. 373) Multidrug resistance (p. 374) Long QT syndrome (p. 388) Signal-transduction pathways and cancer (p. 416) Monoclonal antibodies as anticancer drugs (p. 416) Protein kinase inhibitors as anticancer drugs (p. 417) G-proteins, cholera and whooping cough (p. 417) Vitamins (p. 438) Triose phosphate isomerase deficiency (p. 454) Excessive fructose consumption (p. 466) Lactose intolerance (p. 467) Galactosemia (p. 468) Aerobic glycolysis and cancer (p. 474) Phosphatase deficiency (p. 512) Defects in the citric acid cycle and the development of cancer (p. 513) Beriberi and mercury poisoning (p. 515) Frataxin mutations cause Friedreich’s ataxia (p. 531) Reactive oxygen species (ROS) are implicated in a variety of diseases (p. 539) ROS may be important in signal transduction (p. 540) IF1 overexpression and cancer (p. 554) Brown adipose tissue (p. 555) Mild uncouplers sought as drugs (p.557) Mitochondrial diseases (p. 557) Glucose 6-phosphate dehydrogenase deficiency causes drug-induced hemolytic anemia (p. 610) Glucose 6-phosphate dehydrogenase deficiency protects against malaria (p. 612) Developing drugs for type 2 diabetes (p. 636) Glycogen-storage diseases (p. 637) Chanarin-Dorfman syndrome (p. 648) Carnitine deficiency (p. 650) Zellweger syndrome (p. 657) Diabetic ketosis (p. 659) Ketogenic diets to treat epilepsy (p. 660) Some fatty acids may contribute to pathological conditions (p. 661) The use of fatty acid synthase inhibitors as drugs (p. 667) Effects of aspirin on signaling pathways (p. 669) Diseases resulting from defects in transporters of amino acids (p. 682) Diseases resulting from defects in E3 proteins (p. 685) Drugs target the ubiquitin-proteasome system (p.687) Using proteasome inhibitors to treat tuberculosis (p. 687) Blood levels of aminotransferases indicate liver damage (p. 691) Inherited defects of the urea cycle (hyperammonemia) (p. 697) Alcaptonuria, maple syrup urine disease, and phenylketonuria (p. 705) CLINICAL APPLICATIONS This icon signals the start of a clinical application in the text. Additional, briefer clinical correlations appear in the text as appropriate
High homocysteine levels and vascular disease(p.726) The brain plays a key role in caloric homeostasis(p.804) Inherited disorders of porphyrin metabolism(p.737) Diabetes is a common metabolic disease often resulting Anticancer drugs that block the synthesis of thymidylate from obesity (p.807) (p.757) Exercise beneficially alters the biochemistry of cells(p.813) Ribonucleotide reductase is a target for cancer therapy Food intake and starvation induce metabolic changes(p.816) (p.759) Ethanol atersenergy metabolism in the liver(p.81) Adenosine deaminase and severe combined immunodefi- ciency (p.760) Antibiotics that target DNA gyrase(p.839) Gout(p.761) Blocking telomerase to treat cancer(p.845) Lesch-Nyhan syndrome(p.761) Huntington disease(p.850) Defective repair of DNA and cancer(p.850) Folic acid and spina bifida (p.762) Detection of carcinogens (Ames test)(p.852) Enzyme activation in some cancers to generate phospho choline(p.770) Translocations can result in diseases(p.855) Excess choline and heart disease(p.771) Antibiotic inhibitors of transcription(p.869) Gangliosides and cholera(p.773) Burkitt lymphoma and B-cell leukemia(p.876 Diseases of defective RNA splicing(p.884) Vanishing white matter disease(p.913) Respiratory distress syndrome and Tay-Sachs disease(p.774) Antibiotics that inhibit protein synthesis(p.914) Ceramide metabolism stimulates tumor growth(p.775) Diphtheria(.14) Phosphatidic acid phosphatase and lipodystrophy (p.776) Ricin,a lethal protein-synthesis inhibitor(p.915) erosis(p.78 Induced pluripotent stem cells(p.947) Mutations in the LDL receptor(p.785) Anabolic steroids(p.951) LDL receptor cycling is regulated(p.787) Color blindness(p.97) The role of HDLin protecting against(p.787) The use of capsaicin in pain management(p.978) Clinical management of cholesterol levels(p.788) Immune-system suppressants(p.994) Bile salts are derivatives of cholesterol (p.789) MHCand transplantation rejection (p.1002) The cytochrome P450 system is protective(p.791) AIDS(p.1003 Autoimmune diseases(p.1005) Immune system and cancer(p.1005) A tase inhibitors in the trea east and ovariar cancer (n 794) Charcot-Marie-Tooth disease(p.1022) Rickets and vitamin D(p.795) Taxol (p.1023) meostasis is a means of regulating body weight
xii High homocysteine levels and vascular disease (p. 726) Inherited disorders of porphyrin metabolism (p. 737) Anticancer drugs that block the synthesis of thymidylate (p. 757) Ribonucleotide reductase is a target for cancer therapy (p. 759) Adenosine deaminase and severe combined immunodeficiency (p. 760) Gout (p. 761) Lesch–Nyhan syndrome (p. 761) Folic acid and spina bifida (p. 762) Enzyme activation in some cancers to generate phosphocholine (p. 770) Excess choline and heart disease (p. 771) Gangliosides and cholera (p. 773) Second messengers derived from sphingolipids and diabetes (p. 773) Respiratory distress syndrome and Tay–Sachs disease (p. 774) Ceramide metabolism stimulates tumor growth (p. 775) Phosphatidic acid phosphatase and lipodystrophy (p. 776) Hypercholesterolemia and atherosclerosis (p. 784) Mutations in the LDL receptor (p. 785) LDL receptor cycling is regulated (p. 787) The role of HDL in protecting against arteriosclerosis (p. 787) Clinical management of cholesterol levels (p. 788) Bile salts are derivatives of cholesterol (p. 789) The cytochrome P450 system is protective (p. 791) A new protease inhibitor also inhibits a cytochrome P450 enzyme (p. 792) Aromatase inhibitors in the treatment of breast and ovarian cancer (p. 794) Rickets and vitamin D (p. 795) Caloric homeostasis is a means of regulating body weight (p. 802) The brain plays a key role in caloric homeostasis (p. 804) Diabetes is a common metabolic disease often resulting from obesity (p. 807) Exercise beneficially alters the biochemistry of cells (p. 813) Food intake and starvation induce metabolic changes (p. 816) Ethanol alters energy metabolism in the liver (p. 819) Antibiotics that target DNA gyrase (p. 839) Blocking telomerase to treat cancer (p. 845) Huntington disease (p. 850) Defective repair of DNA and cancer (p. 850) Detection of carcinogens (Ames test) (p. 852) Translocations can result in diseases (p. 855) Antibiotic inhibitors of transcription (p. 869) Burkitt lymphoma and B-cell leukemia (p. 876) Diseases of defective RNA splicing (p. 884) Vanishing white matter disease (p. 913) Antibiotics that inhibit protein synthesis (p. 914) Diphtheria (p. 914) Ricin, a lethal protein-synthesis inhibitor (p. 915) Induced pluripotent stem cells (p. 947) Anabolic steroids (p. 951) Color blindness (p. 974) The use of capsaicin in pain management (p. 978) Immune-system suppressants (p. 994) MHC and transplantation rejection (p. 1002) AIDS (p. 1003) Autoimmune diseases (p. 1005) Immune system and cancer (p. 1005) Vaccines (p. 1006) Charcot-Marie-Tooth disease (p. 1022) Taxol (p. 1023)