MCAT® Biochemistry Review Edited by Alexander Stone Macnow, MD Table of Contents MCAT® Biochemistry Review Cover Title Page Table of Contents The Kaplan MCAT Review Team About Scientific American About the MCAT How This Book Was Created Using This Book Chapter 1: Amino Acids, Peptides, and Proteins Amino Acids, Peptides, and Proteins Introduction 1.1 Amino Acids Found in Proteins 1.2 Acid–Base Chemistry of Amino Acids 1.3 Peptide Bond Formation and Hydrolysis 1.4 Primary and Secondary Protein Structure 1.5 Tertiary and Quaternary Protein Structure 1.6 Denaturation Conclusion 10 Concept Summary 11 Answers to Concept Checks 12 Equations to Remember 13 Shared Concepts 14 Practice Questions 15 Answers and Explanations Chapter 2: Enzymes Enzymes Introduction 2.1 Enzymes as Biological Catalysts 2.2 Mechanisms of Enzyme Activity 2.3 Enzyme Kinetics 2.4 Effects of Local Conditions on Enzyme Activity 2.5 Regulation of Enzyme Activity Conclusion Concept Summary 10 Answers to Concept Checks 11 Equations to Remember 12 Shared Concepts 13 Practice Questions 14 Answers and Explanations Chapter 3: Nonenzymatic Protein Function and Protein Analysis Nonenzymatic Protein Function and Protein Analysis Introduction 3.1 Cellular Functions 3.2 Biosignaling 3.3 Protein Isolation 3.4 Protein Analysis Conclusion Concept Summary Answers to Concept Checks 10 Equations to Remember 11 Shared Concepts 12 Practice Questions 13 Answers and Explanations Chapter 4: Carbohydrate Structure and Function Carbohydrate Structure and Function Introduction 4.1 Carbohydrate Classification 4.2 Cyclic Sugar Molecules 4.3 Monosaccharides 4.4 Complex Carbohydrates Conclusion Concept Summary Answers to Concept Checks 10 Equations to Remember 11 Shared Concepts 12 Practice Questions 13 Answers and Explanations Chapter 5: Lipid Structure and Function Lipid Structure and Function Introduction 5.1 Structural Lipids 5.2 Signaling Lipids 5.3 Energy Storage Conclusion Concept Summary Answers to Concept Checks Shared Concepts 10 Practice Questions 11 Answers and Explanations Chapter 6: DNA and Biotechnology DNA and Biotechnology Introduction 6.1 DNA Structure 6.2 Eukaryotic Chromosome Organization 6.3 DNA Replication 6.4 DNA Repair 6.5 Recombinant DNA and Biotechnology Conclusion Concept Summary 10 Answers to Concept Checks 11 Shared Concepts 12 Practice Questions 13 Answers and Explanations Chapter 7: RNA and the Genetic Code RNA and the Genetic Code Introduction 7.1 The Genetic Code 7.2 Transcription 7.3 Translation 7.4 Control of Gene expression in Prokaryotes 7.5 Control of Gene Expression in Eukaryotes Conclusion Concept Summary 10 Answers to Concept Checks 11 Shared Concepts 12 Practice Questions 13 Answers and Explanations Chapter 8: Biological Membranes Biological Membranes Introduction 8.1 Fluid Mosaic Model 8.2 Membrane Components 8.3 Membrane Transport 8.4 Specialized Membranes Conclusion Concept Summary Answers to Concept Checks 10 Equations to Remember 11 Shared Concepts 12 Practice Questions 13 Answers and Explanations 10 Chapter 9: Carbohydrate Metabolism I: Glycolysis, Glycogen, Gluconeogenesis, and the Pentose Phosphate Pathway Carbohydrate Metabolism I: Glycolysis, Glycogen, Gluconeogenesis, and the Pentose Phosphate Pathway Introduction 9.1 Glucose Transport 9.2 Glycolysis 9.3 Other Monosaccharides 9.4 Pyruvate Dehydrogenase 9.5 Glycogenesis and Glycogenolysis 9.6 Gluconeogenesis 9.7 The Pentose Phosphate Pathway 10 Conclusion 11 Concept Summary 12 Answers to Concept Checks 13 Shared Concepts 14 Practice Questions 15 Answers and Explanations 11 Chapter 10: Carbohydrate Metabolism II: Aerobic Respiration Carbohydrate Metabolism II: Aerobic Respiration Introduction 10.1 Acetyl-CoA 10.2 Reactions of the Citric Acid Cycle 10.3 The Electron Transport Chain 10.4 Oxidative Phosphorylation Conclusion Concept Summary Answers to Concept Checks 10 Shared Concepts 11 Practice Questions 12 Answers and Explanations 12 Chapter 11: Lipid and Amino Acid Metabolism Lipid and Amino Acid Metabolism Introduction 11.1 Lipid Digestion and Absorption 11.2 Lipid Mobilization 11.3 Lipid Transport 11.4 Cholesterol Metabolism 11.5 Fatty Acids and Triacylglycerols 11.6 Ketone Bodies 11.7 Protein Catabolism 10 Conclusion 11 Concept Summary 12 Answers to Concept Checks 13 Shared Concepts 14 Practice Questions 15 Answers and Explanations 13 Chapter 12: Bioenergetics and Regulation of Metabolism Bioenergetics and Regulation of Metabolism Introduction 12.1 Thermodynamics and Bioenergetics 12.2 The Role of ATP 12.3 Biological Oxidation and Reduction 12.4 Metabolic States 12.5 Hormonal Regulation of Metabolism 12.6 Tissue-Specific Metabolism 12.7 Integrative Metabolism 10 Conclusion 11 Concept Summary 12 Answers to Concept Checks 13 Equations to Remember 14 Shared Concepts 15 Practice Questions 16 Answers and Explanations 14 About This Book Copyright Information Glossary Index Art Credits Special Offer for Kaplan Students The Kaplan MCAT Review Team Alexander Stone Macnow, MD Editor-in-Chief Tyra Hall-Pogar, PhD Editor Bela G Starkman, PhD Editor Joshua D Brooks, PhD Kaplan MCAT Faculty Alisha Maureen Crowley Kaplan MCAT Faculty Samer T Ismail Kaplan MCAT Faculty Kelly Kyker-Snowman, MS Kaplan MCAT Faculty Christopher Lopez Kaplan MCAT Faculty MCAT faculty reviewers Elmar R Aliyev; James Burns; Jonathan Cornfield; Nikolai Dorofeev, MD; Benjamin Downer, MS; Colin Doyle; M Dominic Eggert; Marilyn Engle; Eleni M Eren; Raef Ali Fadel; Scott Huff; Elizabeth A Kudlaty; Ningfei Li; John P Mahon; Matthew A Meier; Nainika Nanda; Caroline Nkemdilim Opene; Kaitlyn E Prenger; Uneeb Qureshi; Derek Rusnak, MA; Kristen L Russell, ME; Michael Paul Tomani, MS; Nicholas M White; Kerranna Williamson, MBA; Allison Ann Wilkes, MS; and Tony Yu Thanks to Kim Bowers; Tim Eich; Samantha Fallon; Owen Farcy; Dan Frey; Robin Garmise; Rita Garthaffner; Joanna Graham; Adam Grey; Allison Harm; Beth Hoffberg; Aaron Lemon-Strauss; Keith Lubeley; Diane McGarvey; Petros Minasi; John Polstein; Deeangelee Pooran-Kublall, MD, MPH; Rochelle Rothstein, MD; Larry Rudman; Sylvia Tidwell Scheuring; Carly Schnur; Karin Tucker; Lee Weiss; and the countless others who made this project possible purines, 168–69 pyrimidines, 168–69 ribose in, 165, 166f ribosomal RNA (rRNA), 217, 221, 227–28 ribozymes, 217 Shine–Dalgarno sequence in mRNA, 228 small nuclear ribonucleoproteins (snRNPs or snurps), 224 small nuclear RNA (snRNA), 222, 224 splicing, 224 start codon, 219, 225, 228 transcription, 214–15, 221–23, 241–42 transfer RNA (tRNA), overview, 216–17 transfer RNA (tRNA), role in translation, 229–33 transfer RNA (tRNA), synthesis, 221 See also Genetic code Rocky Balboa, 71 S Salinity, effects on enzyme activity, 50, 58 Saponification, 147, 148, 152 Sarcolemma, 270 Saturated fatty acids, 137, 258, 371, 384 Saturation kinetics, 45, 58 SDS–PAGE (sodium dodecyl sulfate–polyacrylamide gel electrophoresis), 83, 93 SDS (sodium dodecyl sulfate, sodium lauryl sulfate), 24 Second messenger cascades, 79, 258, 406, 409 Selectins, 74–75, 92 Sequencing of DNA, 18, 192–93 Sequencing of primary structure of proteins, 18, 89, 94 Serine, 7, 21 Sesquiterpenes, 142 Severe combined immunodeficiency (SCID), 193 Shine–Dalgarno sequence, 228 Shuttle mechanisms acetyl-CoA shuttle, 372 carnitine shuttle, 374, 385 citrate shuttle, 370 glycerol 3-phosphate shuttle, 344, 351 malate–aspartate shuttle, 345, 351 NADH shuttles, 343–44, 351 Q cycle, 343 Sickle cell anemia, Signaling lipids, 141–46, 151–52 Silent mutations, 219 Single-stranded DNA binding protein, 178, 199 Size-exclusion chromatography, 86–87, 93 Skeletal muscle, metabolic role overview, 416 Small nuclear ribonucleoproteins (snRNPs, or “snurps”), 224 Small nuclear RNA (snRNA), 222, 224 Soaps, 147–49, 152 Sodium–potassium pump (Na+/K+ ATPase), 270–71 Solvation layer, 21 Southern blotting, 192, 201 Specificity of enzymes, 38, 42, 57, 119 Spermaceti, 135 Sphingoid compounds, 138 Sphingolipids, 137, 138–39, 151, 259 Sphingomyelins, 138, 151, 139 Sphingosine, 137, 138 Spliceosome, 224 Standard-state conditions, 396 Starches, 119–20, 300, 301f Start codon, 219, 225, 228 Steroid hormones, 143, 410–11 Steroids, 142–43, 143f, 151, 260 Sterols, 135 Stop codons, 219, 225, 230 Structural genes, 232 Structural lipids, 136–41, 151 Structural proteins, 72, 92 See also specific types Substrate-level phosphorylation, 292, 293, 313 Substrates, 42 Succinate-CoQ oxidoreductase, 342, 350 Succinate dehydrogenase, 335, 342, 350 Succinate formation, 334–35 Succinyl-CoA formation, 334 Succinyl-CoA synthetase, 334–35, 350 Sucrose, 117, 118f, 297 Supercoiling of DNA, 173, 178, 199 Surfactants, 148 Symports, 268 T TATA box, 222, 223 Tautomerization, 114 Telomerase, 175 Telomeres, 175, 182, 199 Temperature, effects on enzyme activity, 49–50, 58, 192 Template strands DNA repair, 183, 185 DNA replication, 178–80 DNA transcription, 214, 215, 221–22 Terpenes, 135, 141–42, 151 Terpenoids, 142 Tetraterpenes, 142 Thermodynamics bioenergetics, overview, 396–98, 421 closed systems, 396 enthalpy changes (ΔH), 21, 265, 397 entropy changes (ΔS), 21, 265, 266, 397 First Law of Thermodynamics, 396 internal energy changes (ΔU ), 396 modified standard state, 397 open systems, 396 standard-state conditions, 396 See also Free energy Thiol group, 7, 328 Thoracic duct, 364 Threonine, Threose structure, 109 Thymine, 168 Thyroid hormones, 406, 412–13 Thyroxine (T4), 412–13 Tight junctions, 263, 275 Tocopherols and tocotrienols, 145 Tollen’s reagent, 113–14 Transcription, 214–15, 221–23, 241–42 Transcription factors, 222, 236, 237–38, 243 Transferases, 39, 57 Transfer RNA (tRNA) anticodons in, 216, 218, 226, 228 base pairing of aminoacyl tRNA with mRNA, 218, 225–26 charged or activated transfer RNA, 216, 217f initiator tRNA, 228 synthesis, 222 Transgenes, 194–95 Transgenic mice, 194–96 Translation elongation, 229, 242 elongation factors (EFs), 229 initiation, 228, 242 initiation factors (IFs), 228 mechanism, 227–30 posttranslational processing, 230–31 release factor (RF), 230 Shine–Dalgarno sequence in mRNA, 228 start codon, 219, 225, 228 synthesis of secretory, membrane, and lysosomal proteins, 230f termination, 230 See also Ribosomes; RNA Transmembrane proteins, 260, 262, 263 Trehalose, 117f Triacylglycerols (triglycerides) digestion and absorption, 362, 364 energy storage, 121, 146–47, 152 fatty acids in, 146–47, 258, 259f mobilization, 365 saponification, 148f, 152 structure, 147–48, 153 synthesis, 373 transport in lipoproteins, 366–68 See also Fatty acids Tricarboxylic acid (TCA) cycle See Citric acid cycle Triiodothyronine (T3), 412–13 Tripeptides, 15 Triterpenes, 142 Trp operon, 232, 234 Truncation mutations, 219 Trypsin, 17, 55, 89, 380 Tryptophan, 6, 7f, 17, 38, 232, 234 Tubulin, 72, 73 Tumor suppressor genes, 183, 200 Tyrosine, 6, 7f, 9, 17, 38 U Uncompetitive inhibition, 53, 58 Uncouplers, 347 Unsaturated fatty acids, 137, 258, 371, 377, 384 Uracil, 168 Urea and denaturation of proteins, 24 Urea cycle, 4, 381–82 UV spectroscopy, 89 V Valine, 3, 5, 6f, 9, 15 Van’t Hoff factor, 267 Very-low-density lipoprotein (VLDL), 258, 415 Viruses, structure, 22 Vitamins as cofactors, 44 ascorbic acid (vitamin C), 44 B complex vitamins, 44 fat-soluble vitamins, 44, 144–45, 149 vitamin A (carotene), 142, 144, 152 vitamin B2 (riboflavin), 44, 402 vitamin D (cholecalciferol), 145, 152 vitamin E, 142, 152 vitamin K, 145, 152 water-soluble vitamins, 44, 144 Von Gierke’s Disease, 304 W Watson–Crick model of DNA structure, 169–71, 198 Waxes, 140f, 260 Wobble position in codons, 219 X X-ray crystallography, 88–89, 93 Z Z-DNA, 171 Zwitterions, 11–12, 12–13, 25, 83–84 Zymogens, 38–39, 55, 59, 380 Art Credits Chapter Cover—Image credited to User: Vossman From Wikimedia Commons Copyright © 2009 Used under license: CC-BY-SA-2.5 Figure 1.12—Image credited to George V Kelvin From The Protein Folding Problem by Frederic M Richards Copyright © 1991 by Scientific American, Inc All rights reserved Figure 1.13—Image 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Alisha Maureen Crowley Kaplan MCAT Faculty Samer T Ismail Kaplan MCAT Faculty Kelly Kyker-Snowman, MS Kaplan MCAT Faculty Christopher Lopez Kaplan MCAT Faculty MCAT faculty reviewers Elmar R Aliyev;.. .MCAT? ? Biochemistry Review Edited by Alexander Stone Macnow, MD Table of Contents MCAT? ? Biochemistry Review Cover Title Page Table of Contents The Kaplan MCAT Review Team About