Biochemistry

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Biochemistry

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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