Biochemistry
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Biochemistry
Biochemistry and the Organization of Cells
How does biochemistry describe life processes? How did living things originate? Chemical Foundations of Biochemistry How and when did the Earth come to be? How were biomolecules likely to have formed on the early Earth? Molecules to Cells: Which came first - the catalysts or the hereditary molecules? The Biggest Biological Distinction-Prokaryotes and Eukaryotes How is prokaryotic DNA organized without a nucleus? Eukaryotic Cells Five Kingdoms, Three Domains Extremophiles: The Toast of the Industry Common Ground for All Cells Did eukaryotes develop from prokaryotes? Did symbiosis play a role in the development of eukaryotes? Biochemical Energetics Energy and Change: What kinds of energy changes take place in living cells? Spontaneity in Biochemical Reactions Life and Thermodynamics Predicting ReactionsWater The Solvent for Biochemical Reactions
Water and Polarity What is polarity? Solvent Properties of Water Hydrogen Bonds Acids, Bases, and pH Titration Curves Buffers How do buffers work? How do we choose a buffer? How do we make buffers in the laboratory? Are naturally occurring pH buffers present in living organisms?Amino Acids and Peptides
Amino Acids Exist in a Three-Dimensional World Individual Amino Acids:Their Structures and Properties Uncommon Amino Acids Amino Acids to Calm Down and Pep Up Amino Acids Can Act as Both Acids and Bases The Peptide Bond Small Peptides with Physiological Activity Phenylketonuria-Little Molecules Have Big Effects Peptide Hormones-More Small Molecules with Big Effects Amino Acids Go Many Different PlacesThe Three Dimensional Structure of Proteins
Protein Structure and Function Primary Structure of Proteins Secondary Structure of Proteins Complete Proteins and Nutrition Periodic Structures in Protein Backbones Secondary Structure of Proteins: Irregularities in Regular Structures Supersecondary Structures and Domains of Proteins The Collagen Triple Helix Two Types of Protein Conformations: Fibrous and Globular Tertiary Structure of Proteins Forces Involved in Tertiary Structures Myoglobin: An Example of Protein Structure Denaturation and Refolding Quaternary Structure of Proteins Protein Folding Dynamics Hydrophobic Interactions:A Case Study in Thermodynamics Protein Folding Dynamics: The Importance of Correct Folding Protein-Folding Chaperones Prions and DiseaseProtein Purification and Characterization Techniques
Extracting Pure Proteins from Cells Column Chromatography What are the different types of chromatography? Electrophoresis Determining the Primary Structure of a Protein Cleavage of the Protein into Peptides Sequencing of Peptides: The Edman Method Protein Purification: Pulling It All TogetherThe Behavior of Proteins Enzymes
Enzymes Are Effective Biological Catalysts Kinetics versus Thermodynamics Enzymes as Markers for Disease Enzyme Kinetic Equations Enzyme-Substrate Binding Examples of Enzyme-Catalyzed Reactions The Michaelis–Menten Approachto Enzyme Kinetics Enzyme Inhibition Practical Information from Kinetic Data Enzyme Inhibition in the Treatment of AIDSThe Behavior of Proteins Enzymes Mechanisms and Control
The Behavior of Allosteric Enzymes The Concerted and Sequential Models for Allosteric Enzymes Control of Enzyme Activity by Phosphorylation Zymogens The Nature of the Active Site Chemical Reactions Involved in Enzyme Mechanisms The Active Site and Transition States Families of Enzymes: Proteases Coenzymes Catalytic Antibodies against Cocaine Catalysts for Green ChemistryLipids and Proteins Are Associated in Biological Membranes
The Definition of a Lipid The Chemical Natures of the Lipid Types What are fatty acids? What are triacylglycerols? What are phosphoacylglycerols? What are waxes and sphingolipids? What are glycolipids? What are steroids? Biological Membranes What is the structure of lipid bilayers? How does the composition of the bilayer affect its properties? Butter versus Margarine-Which Is Healthier? The Kinds of Membrane Proteins The Fluid-Mosaic Model of Membrane Structure Membranes in Drug Delivery The Functions of Biological Membranes Lipid Droplets Are Not Just Great Balls of Fat Lipid-Soluble Vitamins and Their Functions Vision Has Great Chemistry Prostaglandins and Leukotrienes Why Should We Eat More Salmon?Nucleic Acids How Structure Conveys Information
Levels of Structure in Nucleic Acids The Covalent Structure of Polynucleotides The DNA Family Tree The Structure of DNA What is the nature of the DNA double helix? Are there other possible conformations of the double helix? How does prokaryotic DNA supercoil into its tertiary structure? How does supercoiling take place in eukaryotic DNA? What Makes a Triple Helix Useful in Drug Design? Denaturation of DNA The Principal Kinds of RNA and Their Structures What kinds of RNA play a role in life processes? What is the role of transfer RNA in protein synthesis? How does ribosomal RNA combine with proteins to form the site of protein synthesis? The Human Genome Project: Treasure or Pandora’s Box? Why Identical Twins Are Not IdenticalBiosynthesis of Nucleic Acids Replication
The Flow of Genetic Information in the Cell Replication of DNA DNA Polymerase Semidiscontinuous DNA Replication DNA Polymerase from E. coli Proteins Required for DNA Replication Proofreading and Repair Why Does DNA Contain Thymine and Not Uracil? Eukaryotic DNA Replication The SOS Response in E. coli Telomerase and CancerTranscription of the Genetic Code The Biosynthesis of RNA
Transcription of the Genetic Code Transcription in Prokaryotes Transcription Regulation in Prokaryotes Transcription in Eukaryotes Transcription Regulation in Eukaryotes Structural Motifs in DNA-Binding Proteins Post transcriptional RNA Modification Lupus: An Autoimmune Disease Involving RNA Processing Ribozymes What are the characteristics of a ribozyme? Proofreading in Transcription? RNA Fills In Another Missing PieceProtein Synthesis Translation of the Genetic Message
Translating the Genetic Message The Genetic Code Codon–Anticodon Pairing and Wobble Amino Acid Activation Prokaryotic Translation Eukaryotic Translation Posttranslational Modification of Proteins Protein Degradation Chaperones: Preventing Unsuitable Associations Silent Mutations Are Not Always Silent How Do We Adapt to High Altitude?Nucleic Acid Biotechnology
Purification and Detection of Nucleic Acids Restriction Endonucleases Cloning What is cloning? What are plasmids? Genetic Engineering Genetic Engineering in Agriculture Human Proteins through Genetic Recombination Techniques Fusion Proteins and Fast Purifications DNA Libraries The Polymerase Chain Reaction DNA Fingerprinting CSI: Biochemistry - Forensic Uses of DNA Testing Sequencing DNA RNA Interference - The Newest Way to Study Genes Genomics and ProteomicsViruses Cancer and Immunology
Viruses What is the structure of a virus? Families of Viruses Virus Life Cycles Why are viruses important? Retroviruses Why are retroviruses important? Viruses are Used for Gene Therapy The Immune System Innate Immunity-The Front Lines of Defense Acquired Immunity: Cellular Aspects T-Cell Functions T-Cell Memory The Immune System: Molecular Aspects The Immune System: Distinguishing Self from Nonself Viral RNAs Outwit the Immune System Cancer Oncogenes Tumor Suppressors Viruses and Cancer Viruses Helping Cure Cancer Attacking the Symptoms instead of the Disease?The Importance of Energy Changes and Electron Transfer in Metabolism
Standard States for Free-Energy Changes A Modified Standard State for Biochemical Applications Living Things Need Energy-How Do They Use It? The Nature of Metabolism Living Things Are Unique Thermodynamic Systems The Role of Oxidation and Reduction in Metabolism Coenzymes in Biologically Important Oxidation-Reduction Reactions Coupling of Production and Use of Energy Coenzyme A in Activation of Metabolic PathwaysCarbohydrates
Sugars: Their Structures and Stereochemistry What is unique about the structures of sugars? What happens if a sugar forms a cyclic molecule? Reactions of Monosaccharides Vitamin C Is Related to Sugars Some Important Oligosaccharides Fruits, Flowers, Striking Colors, and Medicinal Uses Too Lactose Intolerance: Why Do So Many People Not Want to Drink Milk? Structures and Functions of Polysaccharides Why Is Dietary Fiber So Good for You? Glycoproteins Low-Carbohydrate Diets Glycoproteins and Blood TransfusionsGlycolysis
The Overall Pathway of Glycolysis Biofuels from Fermentation Conversion of Six-Carbon Glucose toThree-Carbon Glyceraldehyde-3-Phosphate Glyceraldehyde-3-Phosphate Is Converted to Pyruvate Anaerobic Metabolism of Pyruvate What Is the Connection between Anaerobic Metabolism and Dental Plaque? Fetal Alcohol Syndrome Energy Production in GlycolysisStorage Mechanisms and Control in Carbohydrate Metabolism
How Glycogen Is Produced and Degraded How does the breakdown of glycogen take place? How is glycogen formed from glucose? How is glycogen metabolism controlled? Why Do Athletes Go In for Glycogen Loading? Gluconeogenesis Produces Glucose from Pyruvate Control of Carbohydrate Metabolism Glucose Is Sometimes Diverted throughthe Pentose Phosphate Pathway The Pentose Phosphate Pathway and Hemolytic AnemiaThe Citric Acid Cycle
The Central Role of the Citric Acid Cycle in Metabolism The Overall Pathway of the Citric Acid Cycle How Pyruvate Is Converted to Acetyl-CoA The Individual Reactions of the Citric Acid Cycle Plant Poisons and the Citric Acid Cycle Energetics and Control of the Citric Acid Cycle The Glyoxylate Cycle: A Related Pathway The Citric Acid Cycle in Catabolism The Citric Acid Cycle in Anabolism Why Can’t Animals Use All the Same Energy Sources as Plants and Bacteria? The Link to Oxygen Why Is It So Hard to Lose Weight?Electron Transport and Oxidative Phosphorylation
The Role of Electron Transport in Metabolism Reduction Potentials in the Electron Transport Chain Organization of Electron Transport Complexes The Connection between Electron Transportand Phosphorylation The Mechanism of Coupling in Oxidative Phosphorylation Respiratory Inhibitors Can Be Usedto Study Electron Transport Shuttle Mechanisms What Does Brown Adipose Tissue Have to Do with Obesity? The ATP Yield from Complete Oxidation of Glucose Sports and Metabolism The Darker Side of SportsLipid Metabolism
Catabolism of Lipids The Energy Yield from the Oxidationof Fatty Acids Catabolism of Unsaturated Fatty Acids and Odd-Carbon Fatty Acids Ketone Bodies Fatty-Acid Biosynthesis Ketone Bodies and Effective Weight Loss Synthesis of Acylglycerols and Compound Lipids A Gene for Obesity Acetyl-CoA Carboxylase-A New Target in the Fight against Obesity? Cholesterol Biosynthesis AtherosclerosisPhotosynthesis
Chloroplasts Are the Site of Photosynthesis The Relationship between Wavelength and Energy of Light Photosystems I and II and the Light Reactions of Photosynthesis Cyclic Electron Transport in Photosystem I Photosynthesis and ATP Production Killing Weeds by Inhibiting Photosynthesis Evolutionary Implications of Photosynthesis with and without Oxygen Dark Reactions of Photosynthesis Fix CO2 Chloroplast Genes CO2 Fixation in Tropical PlantsThe Metabolism of Nitrogen
Nitrogen Metabolism: An Overview Nitrogen Fixation Why Is the Nitrogen Content of Fertilizers So Important? Feedback Inhibition in Nitrogen Metabolism Amino Acid Biosynthesis Essential Amino Acids Amino Acid Catabolism Water and the Disposal of Nitrogen Wastes Chemotherapy and Antibiotics - Taking Advantage of the Need for Folic Acid Purine Biosynthesis Purine Catabolism Lesch-Nyhan Syndrome Pyrimidine Biosynthesis and Catabolism Conversion of Ribonucleotides to Deoxyribonucleotides Conversion of dUTP to dTTPIntegration of Metabolism Cellular Signaling
Connections between Metabolic Pathways Biochemistry and Nutrition What are required nutrients? Why do we need vitamins? What are minerals? The Food Pyramid What is obesity? Alcohol Consumption and Addiction Iron: An Example of a Mineral Requirement Hormones and Second Messengers What are hormones? How do second messengers work? Cyclic AMP and G Proteins Calcium Ion as a Second Messenger Receptor Tyrosine Kinases Hormones and the Control of Metabolism Insulin and Its Effects Insulin and Low-Carbohydrate Diets A Workout a Day Keeps Diabetes Away? The Search for LongevityLiving Cell
Living Cell Types of Living cells Sub cellular Organelles Cell Membrane and its Functions Cell Wall and its Functions Nucleus and its Functions Mitochondria and its Functions Endoplasmic reticulum and its Functions Golgi apparatus and its Functions Ribosomes and its Functions Lysosomes and its Functions Peroxisomes and its Functions Cytoplasm and its Functions Chloroplasts and its Functions Cell Vacuoles Blood: Composition and Functions Formation of blood Body Fluids Buffers Uses of buffer Buffers of blood Acids and basesBiomolecules
Biomolecule: Carbohydrates Classification and Functions of Carbohydrates Proteins: Definition, Classification, Functions Lipids: Definition, Classification, Functions Nucleic acids: Definition, Classification, FunctionsEnzymes
Enzymes Chemical nature of enzymes Naming of enzymes Classification of enzymes Factors influencing enzyme activity Types of enzyme inhibition Iso enzymes Importance of enzymesCarbohydrates
Functions of carbohydrates Classification of carbohydrates Monosaccharides Physical properties of monosaccharides Chemical properties of glucose Haworth projection formula of glucose and fructose Disaccharides Poly saccharidesProteins
Proteins and Sources of protein Amino acids Properties of amino acids Classification of amino acids Physical and Chemical Properties of proteins Protein structure Biologically important proteinsLipids
Lipids Classification of Fatty acids Essential fatty acid (EFA): Structure, Functions Structure of triacyl glycerol Physical and Chemical Properties of triacyl glycerol Phospholipids Classification of Phospholipids Properties of glycero phospholipids and sphingo phospholipids Importance of phospholipids Sterols Cholesterol: Structure, PropertiesNucleic Acids
Structure and Properties of pyrimidine bases Purine bases: Structure and Properties Nucleic acids Nucleic acids: Nucleosides and Nucleotides Structure of DNA Functions of DNA Structure and types of RNAVitamins
Vitamins Fat soluble vitamins Water soluble vitamins Vitamin - A Vitamin D Vitamin E Vitamin K Thiamine (B1) Riboflavin (B2) Niacin (B3) Pyridoxine (B6) Folic acid Vitamin B12 Pantothenic acid (B5) Biotin Vitamin C (Ascorbic Acid)Minerals
Minerals Introduction Calcium Phosphorus Sodium Potassium Chlorine Magnesium Sulphur Iron Copper Iodine Fluorine Zinc Cobalt Manganese Chromium Molybdenum SeleniumBiochemical Techniques
Chromatography Types of chromatography Column chromatography: Types, Principle Thin Layer chromatography Paper chromatography Applications of chromatography Electrophoresis: principle, Types Centrifugation techniques: Principle, Types, Uses Differential centrifugation technique Spectrophotometry The photoelectric colorimeter Applications of spectrophotometryCell Membrane
Cell Membrane: Introduction Cell Membrane: Chemical Composition Models proposed for the plasma membrane Membrane Transport Cell Membrane: Viscosity Surface tension Osmosis and Biological Significance BuffersDigestion
Biochemistry: Digestion Carbohydrates in Digestion Digestion of Proteins Digestion of Lipids Digestion of Nucleic acidsCarbohydrate Metabolism
Biochemistry: Carbohydrate Metabolism Carbohydrate as a source of energy Tricarboxylic acid cycle (TCA cycle) HMP shunt pathway Glycogen Glycogen biosynthesis Degradation of glycogen (Glycogenolysis) Gluconeogenesis Diabetes MellitusProtein Metabolism
Protein Metabolism Protein biosynthesis Protein Metabolism Translation Metabolism of Proteins Urea Cycle Formation of Niacin Formation of Melanin Formation of thyroid hormone Formation of catecholaminesLipid Metabolism
Lipid Metabolism Biological functions of Lipids Fatty acids Biosynthesis of fatty acids Oxidation of Fatty Acids Cholesterol Biosynthesis Biosynthesis of cholesterol Important products derived from cholesterol Biosynthesis of phospholipids Cephalin AtherosclerosisNucleic Acid Metabolism
Nucleic Acid Metabolism Biosynthesis of DNA Replication and Models of Replication Sequential Process of Replication Initiation of DNA replication Catabolism of DNA by Deoxyribonucleases Biosynthesis of RNA (Transcription) Processing of mRNA molecules mRNA Processing of tRNA Molecules Role of tRNA in protein synthesisInborn Errors of Metabolism
Inborn Errors of Metabolism Galactosemia: Causes, Symptoms Von - Gierke’s Disease : Cause, Symptoms Hemophilia: Causes, Symptoms Albinism Alkaptonuria: Causes, Symptoms Taysach’s Disease: Causes, Symptoms NeoplasmBiological Oxidation
Biological Oxidation Redox Couple Electron transport chain Oxidative phosphorylation High energy compoundsEnzyme Kinetics
Enzyme Kinetics Derivation of M - M Equation Enzyme Action Enzyme Inhibitor - ConceptsImmunology
Immunology Infections Immunity Natural Immunity Acquired immunity Humoral immunity Cell mediated immunity Antigens Structure and Types of Antigens Factors influencing the antigenicity of antigens Antibodies Antibody Structure Immunoglobulin and their functions, Types Antigen antibody reactions Blood groupsPracticals
Collection of Blood Preparation of Starch From Potatoes Preparation of Casein From Milk Estimation of Protein (Biuret Method) - Colorimetric Estimation Estimation of Glucose (Orthotoluidine method) Estimation of Calcium (Titrimetric Method) Determination of Blood Grouping
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