GRE Biochemistry, Cell and Molecular Biology (REA) - The Best Test Prep

  TABLE OF CONTENTS   INTRODUCTION Chemical Bonds and Energy Conservation  Thermodynamics and Energy Conservation  Potential Energy Curve  Redox States Water, pH, Acid-Base Reactions, and Buffers  Structure of Water  Acid-Base Reactions  Concept of Acids and Bases in Relationship to pH  Buffers  Biomolecular Structures  Amino Acids and Proteins  Structure of Proteins  Primary Structure  Secondary Structure  a-Helix  ß-Pleated sheets  ß-Turns  Tertiary Structure  Quaternary Structure  Chemical and Enzymatic Reaction Mechanisms  Chemical Reaction Mechanisms    PART 1: BIOCHEMISTRY Contents Introduction  About This Book About REA's Test Experts About the Test Format of the GRE Biochemistry, Cell and Molecular Biology Test Scoring the Test  Score Conversion Chart  Test-Taking Strategies  The Day of the Test During the Test Study Schedule  First-Order Reactions  Second-Order Reactions  Some Factors That Influence Reaction Rates  Enzymatic Reaction Mechanisms  How Does an Enzyme Help Lower the Energy/Heat of Activation of a Reaction  Proximity and Orientation  Covalent Catalysis  Strain and Distortion  Acid-Base Catalysis  Selected List of Coenzymes and Their Roles in Catalysis  Classification of Enzymes by the Types of Reactions They Catalyze  Oxidoreductases  Transferases  Hydrolases  Lyases  Isomerases  Ligases  Enzyme Kinetics  Practical Aspect of Initial Velocity Measurement  Lineweaver-Burk Plots  Diagnostic Value of Lineweaver-Burk Plots: Enzyme Inhibition  Classification of the Types of Enzyme Inhibitors  Mechanism-Based Inhibitors  Two-Substrate Reactions  Sequential Reactions May Be Either Random or Ordered Ping-Pong or Double-Displacement Reactions  Antibodies as Catalysts  Regulation of Enzymatic Activity  Summary of Regulatory Mechanisms  Kinetic Models for Allosteric Regulation  Kinetic Description of Allosteric Interactions: The Concerted Model  Significance of the Hill Coefficient  Metabolism  Forms of Conserved Energy in Metabolism  Glycolysis  Reaction That Commits Glucose Metabolism to Glycolysis  Aldolase Catalyzes the Production of Two -Carbon Compounds from Fru ,-P  Triose Phosphate Isomerase  Glyceraldehyde -Phosphate Dehydrogenase (GAPDH) Reaction  Phosphoglycerate Kinase Reaction  Phosphoglycerate Mutase Reaction  Enolase Catalyzes the Second “High-Energy” Compound in Glycolysis  Pyruvate Kinase Generates the Second ATP Molecule in Glycolysis  Summary of Glycolysis  Pyruvate Metabolism: Formation of Acetylcoenzyme A  The Tricarboxyclic Acid Cycle (TCA Cycle)  Regulation of the TCA cycle  Anaplerotic Reactions for the TCA Cycle  Oxidative Phosphorylation  Pentose Phosphate Pathway  Oxidative Phase of the Pentose Phosphate Pathway  Nonoxidative Phase of the Pentose Phosphate Pathway  Glucuronic Acid Oxidative Pathway  Gluconeogenesis and Glycogenesis  Summary of Entry Points in the TCA Cycle and Glycolysis That Can Lead to Gluconeogenesis  Glycogen Metabolism  Glycogenesis  Glycogenolysis  Regulation of Glycogen Metabolism  Photosynthesis  Photochemical Consideration of Light Absorption and Energy Generation  Light Independent Reactions of Photosynthesis: The Calvin Cycle  Adaptive Photosynthetic Mechanisms  Nitrogen Metabolism  Nitrogen Fixation  Chemical Reactions of Pyridoxyl Phosphate Relative to Amino Acid Metabolism  Biosynthesis of Amino Acids  Amino Acids Derived from Oxaloacetate/Aspartate  Amino Acids Derived from -Phosphoglycerate  Cysteine  Serine  Glycine  Amino Acids Derived from Pyruvate Amino Acids Derived from a-Ketoglutarate  Amino Acids Derived from Phosphoenolpyruvate and Erythrose--phosphate  Histidine  Degradation of Amino Acids  Methionine  The Urea Cycle  Nucleotide Structure and Metabolism  Synthesis of Purines  Summary of Key Points About Purine Biosynthesis  Degradation of Purines  Synthesis of Pyrimidines  Synthesis of Deoxyribonucleotides  Regulation of Ribonucleotide Reductase Activity  Thymine Biosynthesis  Degradation of Pyrimidines  Heme Metabolism  Heme and Chlorophyll Biosynthesis  Heme and Chlorophyll Degradation  Lipid Metabolism  Fatty Acid Biosynthesis  Elongation of Palmitic Acid  Formation of Unsaturated Fatty Acids  Nomenclature and Other Positions Where Desaturases Function  Arachiodonic Acid and Signaling/Regulatory Molecules  Cholesterol and Steroid Hormones Are Derived from Acetate  Fatty Acids Are Stored as Triglycerides  Sphingolipids  Fatty Acid Oxidation  Special Cases to Consider for b-Oxidation of Fatty Acids  Methods  Methods for Cell Disruption  Mechanical Methods  Nonmechanical Methods of Cell Disruption  Separation of Cellular Components by Centrifugation  Centrifugal Force Required to Pellet Selected Cellular Components  Purification of Soluble Proteins Chromatography  Ion Exchange Chromatography  Hydrophobic Interaction Chromatography  Gel Filtration Chromatography  Affinity Chromatography  High Performance Liquid Chromatography (HPLC)  Isotopes Used to Study Biological Systems  Radioactive Isotopes  Stable Isotopes  Relationship of Solute Concentration to Its Absorbance of Light  Absorbance of Light and the Lambert-Beer Law  Sample Analyses by Electrophoresis  Polyacrylamide Gel Electrophoresis (PAGE)  Two-Dimensional Gel Electrophoresis  Determination of Molecular Mass Using SDS Denaturing Gels  Western Blot Analysis Cellular Compartments of Prokaryotes and Eukaryotes  Organization, Dynamics, and Functions  Microscopy  General Introduction to Prokaryotes and Eukaryotes  Prokaryotes  Eukaryotes  Cell Death  Apoptosis  Necrosis  Cellular Membrane Systems (Structure and Transport)  Prokaryotic Cells, Plasma Membrane, and Cell Wall  Eukaryotic Plasma Membranes and Cell Walls  Membrane Biogenesis  Membrane Transport  Inactive Transport  Active Transport  Exo- and Endocytosis    PART 2:  CELL BIOLOGY Nucleus (Envelope and Matrix) and Chromosomes  Prokaryotic Cells—Chromosome  Eukaryotic Cells—Chromosomes and Nucleus  Other Intracellular Structures, Including Mitochondria and Chloroplasts  Prokaryotes  Eukaryotes  Specialized Structures and Other Characteristics  Cell Dynamics  Cell Surface and Cell Communication  Extracellular Matrix  The Extracellular Matrix of Connective Tissue  Connective Tissue  The Proteins of Connective Tissue  The Extracellular Matrix of Endothelial Tissue  Cell–Cell Interaction  Binding of Cells to the Extracellular Matrix  Communication between Extracellular Matrix and Cytoskeleton  Cell Adhesion and Junctions: Cell–Cell Communication  Signal Transduction and Receptor Function  Cell Membrane Receptors  Second Messenger Systems  The cAMP Pathway  The Phosphatidylinositol Pathway  G-Protein-Associated Ion Channels  Receptors That Are Enzymes  Steroid and Thyroid Hormones  Excitable Membrane Systems  Cytoskeleton, Motility, and Shape Actin Filaments  Actin in Muscle Contraction  Microtubules  Intermediate Filaments  Organization of the Cytoskeleton  Cell Surface Structures of Prokaryotes  Protein Synthesis and Processing  Cell Division, Differentiation, and Development  Bacterial Cell Division  Eukaryotic Cell Cycle  Mitosis and Cytokinesis  Cytokinesis  Growth Factors  Meiosis and Gametogenesis  Fertilization and Early Embryonic Development  Fertilization  Embryogenesis  Early Mammalian Development  From Gastrula to Fully Developed Organism  Positional Information  Nuclear/Cytoplasmic Interactions  Tissue-Specific Expression    PART 3:  MOLECULAR BIOLOGY Mendelian and Non-Mendelian Inheritance  Punnett Square Diagrams  Transformation, Transduction, and Conjugation  Recombination and Complementation  Mutational Analysis  Genetic Mapping and Linkage Analysis  Chromatin and Chromosomes  Karyotypes  Translocations, Inversions, Deletions, and Duplications  Aneuploidy and Polyploidy  Structure  Genomics  Genome Structure  Repeated DNA and Gene Families  Centromeres and Telomeres  Gene Identifi cation  Transposable Elements  Gene Maintenance  DNA Replication  The Challenges of DNA Replication  DNA Damage and Repair DNA Modifi cation  DNA Recombination and Gene Conversion  Branch Migration  Gene Conversion  The Genetic Code  Transcription  Gene Regulation in Prokaryotes  Positive and Negative Control of the Operon  Gene Regulation in Eukaryotes  Cis- and Trans-Acting Regulatory Elements  Gene Rearrangements and Amplifi cation  Bacteriophages and Animal and Plant Viruses  Genome Replication and Regulation  Virus-Host Interactions  Methodology  Restriction Maps  DNA Cloning in Prokaryotes and Eukaryotes  Other Uses of Restriction Endonucleases  Nucleic Acid Blotting and Hybridization  PCR  Sequencing and Analysis  Protein-Nucleic Acid Interaction  Site-Directed Mutagenesis  Answer to Mapping Problem  Practice Exams  Answer Sheet: Practice Exam   Practice Exam   Answer Key  Detailed Explanations of Answers  Answer Sheet: Practice Exam   Practice Exam   Answer Key  Detailed Explanations of Answers  Index