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 Reactions

Water 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 Places

The 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 Disease

Protein 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 Together

The 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 AIDS

The 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 Chemistry

Lipids 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 Identical

Biosynthesis 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 Cancer

Transcription 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 Piece

Protein 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 Proteomics

Viruses 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 Pathways

Carbohydrates


=> 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 Transfusions

Glycolysis


=> 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 Glycolysis

Storage 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 Anemia

The 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 Sports

Lipid 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
=> Atherosclerosis

Photosynthesis


=> 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 Plants

The 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 dTTP

Integration 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 Longevity

Living 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 bases

Biomolecules


=> Biomolecule: Carbohydrates
=> Classification and Functions of Carbohydrates
=> Proteins: Definition, Classification, Functions
=> Lipids: Definition, Classification, Functions
=> Nucleic acids: Definition, Classification, Functions

Enzymes


=> Enzymes
=> Chemical nature of enzymes
=> Naming of enzymes
=> Classification of enzymes
=> Factors influencing enzyme activity
=> Types of enzyme inhibition
=> Iso enzymes
=> Importance of enzymes

Carbohydrates


=> Functions of carbohydrates
=> Classification of carbohydrates
=> Monosaccharides
=> Physical properties of monosaccharides
=> Chemical properties of glucose
=> Haworth projection formula of glucose and fructose
=> Disaccharides
=> Poly saccharides

Proteins


=> 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 proteins

Lipids


=> 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, Properties

Nucleic 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 RNA

Vitamins


=> 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
=> Selenium

Biochemical 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 spectrophotometry

Cell 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
=> Buffers

Digestion


=> Biochemistry: Digestion
=> Carbohydrates in Digestion
=> Digestion of Proteins
=> Digestion of Lipids
=> Digestion of Nucleic acids

Carbohydrate 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 Mellitus

Protein 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 catecholamines

Lipid 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
=> Atherosclerosis

Nucleic 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 synthesis

Inborn 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
=> Neoplasm

Biological Oxidation


=> Biological Oxidation
=> Redox Couple
=> Electron transport chain
=> Oxidative phosphorylation
=> High energy compounds

Enzyme Kinetics


=> Enzyme Kinetics
=> Derivation of M - M Equation
=> Enzyme Action
=> Enzyme Inhibitor - Concepts

Immunology


=> 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 groups

Practicals


=> 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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