Biochemistry Tymockzo, Berg, & Stryer • 5th Edition • 9780716798071

Ch. 1 - Prelude: Biochemistry and the Genomic Revolution

What is Biochemistry? Characteristics of Life Abiogenesis Nucleic Acids Carbohydrates Lipids Proteins Taxonomy Cell Organelles Endosymbiotic Theory Central Dogma Functional Groups Chemical Bonds Organic Chemistry Entropy Second Law of Thermodynamics Equilibrium Constant Gibbs Free Energy Properties of Water Osmosis Hydrophobic Effect Acids and Bases Autoionization of Water pH Acid Dissociation Constant Henderson Hasselbalch Equation Determining Predominate Species Titration Buffer Solution

Ch. 3 - Protein Structure and Function

Amino Acid Groups Amino Acid Three Letter Code Amino Acid One Letter Code Amino Acid Configuration Essential Amino Acids Nonpolar Amino Acids Aromatic Amino Acids Polar Amino Acids Charged Amino Acids How to Memorize Amino Acids Zwitterion Non-Ionizable Vs. Ionizable R-Groups Isoelectric Point Isoelectric Point of Amino Acids with Ionizable R-Groups Titrations of Amino Acids with Non-Ionizable R-Groups Titrations of Amino Acids with Ionizable R-Groups Amino Acids and Henderson-Hasselbalch Peptide Bond Primary Structure of Protein Altering Primary Protein Structure Drawing a Peptide Determining Net Charge of a Peptide Isoelectric Point of a Peptide Approximating Protein Mass Peptide Group Ramachandran Plot Atypical Ramachandran Plots Alpha Helix Alpha Helix Pitch and Rise Alpha Helix Hydrogen Bonding Alpha Helix Disruption Beta Strand Beta Sheet Antiparallel and Parallel Beta Sheets Beta Turns Tertiary Structure of Protein Protein Motifs and Domains Denaturation Anfinsen Experiment Protein Folding Chaperone Proteins Quaternary Structure Simple Vs. Conjugated Proteins Fibrous and Globular Proteins

Ch. 4 - Exploring Proteins

Protein Purification Protein Extraction Differential Centrifugation Salting Out Dialysis Column Chromatography Ion-Exchange Chromatography Anion-Exchange Chromatography Size Exclusion Chromatography Affinity Chromatography Specific Activity HPLC Spectrophotometry Native Gel Electrophoresis SDS-PAGE SDS-PAGE Strategies Isoelectric Focusing 2D-Electrophoresis Diagonal Electrophoresis Mass Spectrometry Mass Spectrum Tandem Mass Spectrometry Peptide Mass Fingerprinting Overview of Direct Protein Sequencing Amino Acid Hydrolysis FDNB Chemical Cleavage of Bonds Peptidases Edman Degradation Edman Degradation Sequenator and Sequencing Data Analysis Edman Degradation Reaction Efficiency Ordering Cleaved Fragments Strategy for Ordering Cleaved Fragments Indirect Protein Sequencing Via Geneomic Analyses Antibody ELISA

Ch. 8 - Enzymes: Basic Concepts and Kinetics

Enzymes Enzyme-Substrate Complex Lock and Key Vs. Induced Fit Models Optimal Enzyme Conditions Activation Energy Types of Enzymes Cofactor Catalysis Electrostatic and Metal Ion Catalysis Covalent Catalysis Reaction Rate Enzyme Kinetics Rate Constants and Rate Law Reaction Orders Rate Constant Units Initial Velocity Vmax Enzyme Km Enzyme Steady-State Conditions Michaelis-Menten Assumptions Michaelis-Menten Equation Lineweaver-Burk Plot Michaelis-Menten vs. Lineweaver-Burk Plots Shifting Lineweaver-Burk Plots Calculating Vmax Calculating Km Kcat Specificity Constant Enzyme Inhibition Irreversible Inhibition Reversible Inhibition Inhibition Constant Degree of Inhibition Apparent Km and Vmax Inhibition Effects on Reaction Rate Competitive Inhibition Uncompetitive Inhibition Mixed Inhibition Noncompetitive Inhibition Recap of Reversible Inhibition Allosteric Regulation Allosteric Kinetics Allosteric Enzyme Conformations Allosteric Effectors Concerted (MWC) Model Sequential (KNF) Model Chymotrypsin Chymotrypsin's Catalytic Mechanism

Ch. 10 - Regulatory Strategies: Enzymes and Hemoglobin

Negative Feedback Positive Feedback Post Translational Modification Ubiquitination Phosphorylation Zymogens Introduction to Protein-Ligand Interactions Protein-Ligand Equilibrium Constants Protein-Ligand Fractional Saturation Myoglobin vs. Hemoglobin Heme Prosthetic Group Hemoglobin Cooperativity Hill Equation Hill Equation Hill Plot Hemoglobin Binding in Tissues & Lungs Hemoglobin Carbonation & Protonation Bohr Effect BPG Regulation of Hemoglobin BPG Regulation of Hemoglobin Fetal Hemoglobin Sickle Cell Anemia

Ch. 21 - Glycogen Metabolism

Glycogen Phosphorylase Liver vs Muscle Glycogen Phosphorylase

Ch. 34 - Molecular Motors

Motor Proteins Skeletal Muscle Anatomy Skeletal Muscle Contraction

Ch. 10 - Regulatory Strategies: Enzymes and Hemoglobin

Protein-Ligand Equilibrium Constants Protein-Ligand Fractional Saturation

Ch. 11 - Carbohydrates

Carbohydrates Monosaccharides Stereochemistry of Monosaccharides Monosaccharide Configurations Cyclic Monosaccharides Hemiacetal vs. Hemiketal Anomer Mutarotation Pyranose Conformations Common Monosaccharides Derivatives of Monosaccharides Reducing Sugars Reducing Sugars Tests Glycosidic Bond Disaccharides Glycoconjugates Polysaccharide Cellulose Chitin Peptidoglycan Starch Glycogen Lectins

Ch. 12 - Lipids and Cell Membranes

Lipids Fatty Acids Fatty Acid Nomenclature Omega-3 Fatty Acids Triacylglycerols Glycerophospholipids Sphingolipids Sphingophospholipids Sphingoglycolipids Sphingolipid Recap Waxes Eicosanoids Isoprenoids Steroids Steroid Hormones Lipid Vitamins Comprehensive Final Map Biological Membranes Physical Properties of Biological Membranes Types of Membrane Proteins Integral Membrane Proteins Peripheral Membrane Proteins Lipid-Linked Membrane Proteins

Ch. 13 - Membrane Channels and Pumps

Biological Membrane Transport Passive vs. Active Transport Passive Membrane Transport Facilitated Diffusion Erythrocyte Facilitated Transporter Models Membrane Transport of Ions Primary Active Membrane Transport Sodium-Potassium Ion Pump SERCA: Calcium Ion Pump ABC Transporters Secondary Active Membrane Transport Glucose Active Symporter Model Endocytosis & Exocytosis Neurotransmitter Release Summary of Membrane Transport Thermodynamics of Membrane Diffusion: Uncharged Molecule Thermodynamics of Membrane Diffusion: Charged Ion

Ch. 15 - Signal Transduction Pathways: An Intro. to Information Metabolism

Introduction to Biosignaling G protein-Coupled Receptors Stimulatory Adenylate Cyclase GPCR Signaling cAMP & PKA Inhibitory Adenylate Cyclase GPCR Signaling Drugs & Toxins Affecting GPCR Signaling Recap of Adenylate Cyclase GPCR Signaling Phosphoinositide GPCR Signaling PSP Secondary Messengers & PKC Recap of Phosphoinositide Signaling Receptor Tyrosine Kinases Insulin Insulin Receptor Insulin Signaling on Glucose Metabolism Insulin Signaling as a Growth Factor Recap of Insulin Signaling Jak-Stat Signaling Lipid Hormone Signaling Summary of Biosignaling Signaling Defects & Cancer

Clutch Review 1: Nucleic Acids, Lipids, & Membranes

Nucleic Acids 1 Nucleic Acids 2 Nucleic Acids 3 Nucleic Acids 4 DNA Sequencing 1 DNA Sequencing 2 Lipids 1 Lipids 2 Membrane Structure 1 Membrane Structure 2 Membrane Transport 1 Membrane Transport 2 Membrane Transport 3 Nucleic Acids 1 Nucleic Acids 2 Nucleic Acids 3 Lipids Membrane Structure 1 Membrane Structure 2 Membrane Transport 1 Membrane Transport 2

Clutch Review 2: Biosignaling, Glycolysis, Gluconeogenesis, & PP-Pathway

Biosignaling 1 Biosignaling 2 Biosignaling 3 Biosignaling 4 Glycolysis 1 Glycolysis 2 Glycolysis 3 Glycolysis 4 Fermentation Gluconeogenesis 1 Gluconeogenesis 2 Pentose Phosphate Pathway Practice - Biosignaling Practice - Bioenergetics 1 Practice - Bioenergetics 2 Practice - Glycolysis 1 Practice - Glycolysis 2 Practice - Gluconeogenesis Practice - Pentose Phosphate Path

Clutch Review 3: Pyruvate & Fatty Acid Oxidation, Citric Acid Cycle, & Glycogen Metabolism

Pyruvate Oxidation Citric Acid Cycle 1 Citric Acid Cycle 2 Citric Acid Cycle 3 Citric Acid Cycle 4 Metabolic Regulation 1 Metabolic Regulation 2 Glycogen Metabolism 1 Glycogen Metabolism 2 Fatty Acid Oxidation 1 Fatty Acid Oxidation 2 Citric Acid Cycle Practice 1 Citric Acid Cycle Practice 2 Citric Acid Cycle Practice 3 Glucose and Glycogen Regulation Practice 1 Glucose and Glycogen Regulation Practice 2 Fatty Acid Oxidation Practice 1 Fatty Acid Oxidation Practice 2

Clutch Review 4: Amino Acid Oxidation, Oxidative Phosphorylation, & Photophosphorylation

Amino Acid Oxidation 1 Amino Acid Oxidation 2 Oxidative Phosphorylation 1 Oxidative Phosphorylation 2 Oxidative Phosphorylation 3 Oxidative Phosphorylation 4 Photophosphorylation 1 Photophosphorylation 2 Photophosphorylation 3 Practice: Amino Acid Oxidation 1 Practice: Amino Acid Oxidation 2 Practice: Oxidative Phosphorylation 1 Practice: Oxidative Phosphorylation 2 Practice: Oxidative Phosphorylation 3 Practice: Photophosphorylation 1 Practice: Photophosphorylation 2