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Biochemistry Biochemistry

Biochemistry Miesfeld • 2nd Edition • 978-0393533507

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Ch. 1 - Principles of Biochemistry

What is Biochemistry? Characteristics of Life Functional Groups Chemical Bonds Organic Chemistry Nucleic Acids Proteins Carbohydrates Lipids Cell Organelles Endosymbiotic Theory Central Dogma

Ch. 2 - Physical Biochemistry: Energy Conversion, Water, and Membranes

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 Membrane Structure 1 Membrane Structure 2

Ch. 3 - Nucleic Acid Structure and Function

Nucleic Acids 1 Nucleic Acids 2 Nucleic Acids 3 Nucleic Acids 4 DNA Sequencing 1 DNA Sequencing 2

Ch. 4a - Protein Structure (Amino Acids)

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

Ch. 4b - Protein Structure (Organization and Folding)

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 Prions Quaternary Structure Simple Vs. Conjugated Proteins Fibrous and Globular Proteins

Ch. 5 - Methods in Protein Biochemistry

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

Ch. 6 - Protein Function

Introduction to Protein-Ligand Interactions Protein-Ligand Equilibrium Constants Protein-Ligand Fractional Saturation Myoglobin vs. Hemoglobin Heme Prosthetic Group Hemoglobin Cooperativity Hill Equation Hill Plot Hemoglobin Binding in Tissues & Lungs Hemoglobin Carbonation & Protonation Bohr Effect BPG Regulation of Hemoglobin Fetal Hemoglobin Sickle Cell Anemia Chymotrypsin Chymotrypsin's Catalytic Mechanism Glycogen Phosphorylase Liver vs Muscle Glycogen Phosphorylase Antibody ELISA Motor Proteins Skeletal Muscle Anatomy Skeletal Muscle Contraction

Ch. 7a - Enzyme Mechanisms (Overview 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

Ch. 7b - Enzyme Mechanisms (Inhibition and Regulation)

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 Negative Feedback Positive Feedback Post Translational Modification Ubiquitination Phosphorylation Zymogens

Ch. 8 - Cell Signaling Systems

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 Recap Of Insulin Signaling in Glucose Metabolism Insulin Signaling as a Growth Factor Recap of Insulin Signaling As A Growth Factor Recap of Insulin Signaling Jak-Stat Signaling Lipid Hormone Signaling Summary of Biosignaling Signaling Defects & Cancer

Ch. 9 - Glycolysis: A Paradigm of Metabolic Regulation

Glycolysis 1 Glycolysis 2 Glycolysis 3 Glycolysis 4 Practice - Glycolysis 1 Practice - Glycolysis 2

Ch, 10 - The Citrate Cycle

Pyruvate Oxidation Citric Acid Cycle 1 Citric Acid Cycle 2 Citric Acid Cycle 3 Citric Acid Cycle 4 Citric Acid Cycle Practice 1 Citric Acid Cycle Practice 2 Citric Acid Cycle Practice 3

Ch. 11 - Oxidative Phosphorylation

Oxidative Phosphorylation 1 Oxidative Phosphorylation 2 Oxidative Phosphorylation 3 Oxidative Phosphorylation 4 Practice: Oxidative Phosphorylation 1 Practice: Oxidative Phosphorylation 2 Practice: Oxidative Phosphorylation 3

Ch. 12 - Photosynthesis

Photophosphorylation 1 Photophosphorylation 2 Photophosphorylation 3 Practice: Photophosphorylation 1 Practice: Photophosphorylation 2

Ch. 13 - Carbohydrates Structure and Function

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. 14 - Carbohydrate Metabolism

Fermentation Gluconeogenesis 1 Gluconeogenesis 2 Pentose Phosphate Pathway Practice - Gluconeogenesis Practice - Pentose Phosphate Path Glycogen Metabolism 1 Glycogen Metabolism 2 Glucose and Glycogen Regulation Practice 1 Glucose and Glycogen Regulation Practice 2

Ch. 15 - Lipid Structure and Function

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 Lipid Map Biological Membranes Physical Properties of Biological Membranes Types of Membrane Proteins Integral Membrane Proteins Peripheral Membrane Proteins Lipid-Linked Membrane Proteins

Ch. 16 - Lipid Metabolism

Fatty Acid Oxidation 1 Fatty Acid Oxidation 2 Fatty Acid Oxidation Practice 1 Fatty Acid Oxidation Practice 2

Ch. 17 - Amino Acid Metabolism

Amino Acid Oxidation 1 Amino Acid Oxidation 2 Practice: Amino Acid Oxidation 1 Practice: Amino Acid Oxidation 2

Ch. 19 - Metabolic Integration

Metabolic Regulation 1 Metabolic Regulation 2