Biochemistry: Fundamentals and Bioenergetics

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Contents
Foreword
Preface
List of Contributors
Scope and Importance of Biological Chemistry
	Nene Takio1, Meera Yadav1,* and Hardeo Singh Yadav1
	INTRODUCTION
	CENTRE OF BIOCHEMICAL REACTIONS
	BRANCHES IN BIOCHEMISTRY
		Enzymology
			Factors Affecting the Enzyme Activity
		Endocrinology
		Molecular Biology
		Molecular Genetics and Genetic Engineering
			Applications of Genetic Engineering
		Structural and Metabolic Biochemistry
	WHY UNDERSTANDING BIOCHEMISTRY IS IMPORTANT?
		Importance of Biochemistry in Medicine
			Drug Designing
			Diagnosis
			Nutrition
		Importance of Biochemistry in Agriculture
		Importance of Biochemistry in Nutrition
		Importance of Biochemistry in Pathology
		Importance of Biochemistry in Pharmacy
			Drug Constitution
			The Half-life
			Drug Storage
			Drug Metabolism
		Importance of Biochemistry in Plants
			Photosynthesis
			Different Sugars
			Plants Secondary Metabolites
	RECENT TRENDS IN BIOCHEMISTRY
		Human Genome Project
			Application and Benefits of Human Genome Project (HGP)
		Environmental Biochemistry
		Biomarkers
		Biosensors
		Latest Developments in Environmentally Friendly Biosensors
		Gene Therapy
	CANCER
	KEYWORDS
		Genome
		Biopsy
		Genotype
		Xenobiotics
		Transgenes
	SHORT-ANSWER TYPE QUESTION
	LONG-ANSWER TYPE QUESTIONS
	MULTIPLE CHOICE QUESTIONS
	CONSENT FOR PUBLICATION
	CONFLICT OF INTEREST
	ACKNOWLEDGEMENTS
	REFERENCES
Structure of Water: Acid-Base and Buffers; Hydrogen Bonding
	Nivedita Rai1, Shilpa Saikia1, Meera Yadav1,* and Hardeo Singh Yadav1
	INTRODUCTION
	PHYSICAL AND CHEMICAL CHARACTERISTIC OF WATER
	ACID AND BASE CONCEPT
		Properties of Acids and Bases According to Robert Boyle
		The Arrhenius Definition of Acids and Bases
			Limitations of Arrhenius Theory
			Bronsted Definition of Acids and Bases
		Conjugate Acids and Bases
		The Acid-Base Chemistry of Water
		Lewis Acid-base Concept
		pH Scale
	HYDROGEN BONDING IN WATER
	TYPES OF HYDROGEN BOND
	HYDROPHOBIC
	HISTORY
	NOMENCLATURE
	SUMMARY
	LONG-ANSWER TYPE QUESTIONS
	SHORT-ANSWER TYPE QUESTION
	MULTIPLE CHOICE QUESTIONS
	CONSENT FOR PUBLICATION
	CONFLICT OF INTEREST
	ACKNOWLEDGEMENTS
	REFERENCES
Electrostatic and Van Der Waals Forces
	Nene Takio1, Dencil Basumatary1, Meera Yadav1,* and Hardeo Singh Yadav1
	INTRODUCTION
	FUNDAMENTAL FORCES IN BIOMOLECULES
		Covalent Bonds
		Non-Covalent Bonds
	HYDROGEN BONDING
	HYDROGEN BONDING AND ITS ROLE IN DNA
	HYDROGEN BONDING IN PROTEINS
	ELECTROSTATIC INTERACTIONS
	ROLE IN PROTEIN FOLDING
	MOLECULAR RECOGNITION
	VANDER WAALS INTERACTIONS
		Dipole-dipole/Keesom Interactions
		Dipole Induced Dipole/Debye Forces
		London Dispersion Forces
	HYDROPHOBIC INTERACTION
		Causes of Hydrophobic Interactions
		Thermodynamics of Hydrophobic Interactions
		Formation of Hydrophobic Interactions
		Strength of Hydrophobic Interactions
			Temperature
			Number of Carbon Atoms on the Molecules
			Shape of Hydrophobes
		Hydrophobic Interactions in Protein Folding
		Zwitterions
			Glycine vs. Carbonic Acid
		Titration Curves
		Buffer Capacity and Buffer Intensity
	ROLE OF FORCES IN BIOMOLECULES
	SUMMARY
	KEYWORDS
		Vander Waals Contact Distance
		Dipole-dipole Interactions
		Thermophiles
		Supramolecules
	SHORT-ANSWER TYPE QUESTION
	LONG-ANSWER TYPE QUESTIONS
	MULTIPLE CHOICE QUESTIONS
	CONSENT FOR PUBLICATION
	CONFLICT OF INTEREST
	ACKNOWLEDGEMENTS
	REFERENCES
Introduction To Physical Techniques for Determination of Structure of Biopolymers
	Nene Takio1, Meera Yadav1,* and SonamTashi Khom1
	INTRODUCTION
	BIOPOLYMER TECHNIQUES
		X-ray Crystallography
			Diffraction in X-ray Crystallography
			Applications
			NMR (Nuclear Magnetic Resonance)
		Electron Microscopy
			Principle of Electron Microscopy
			Types of Electron Microscopy
			Transmission Microscopy (TEM)
	SEM VS. TEM
		SEM vs. TEM Advantages
		Compared to SEMs, TEMs
		Electron Tomography
	SUMMARY
	KEYWORDS
		Mosaicity
		Pleomorphism
		Fourier Transforms
		Synchrotrons
	SHORT-ANSWER TYPE QUESTION
	LONG-ANSWER TYPE QUESTIONS
	MULTIPLE CHOICE QUESTIONS
	CONSENT FOR PUBLICATION
	CONFLICT OF INTEREST
	ACKNOWLEDGEMENTS
	REFERENCES
Structure and Function of Biological Biomolecules: Carbohydrates, Amino Acids, Proteins, Nucleic Acids, Lipids and Biomembranes
	Nagendra Nath Yadav1,*, Saroj Yadav2 and Archana Pareek1
	CARBOHYDRATES
		Synthesis of Carbohydrates
		Function of Carbohydrates
		Classification
			Based on their Behavior Upon Hydrolysis
			Based on their Taste
			Based on their Reaction (Oxidation)
	CLASSIFICATION OF MONOSACCHARIDES
	STRUCTURE OF MONOSACCHARIDES
	D & L CONFIGURATION (RELATIVE CONFIGURATION)
	ENANTIOMER
		Optical activity of sugars: (d+) or (l-) form
		Racemic mixture: (±) or (d, l) form
	ABSOLUTE CONFIGURATION (R, S - FORM)
	FISCHER PROJECTION FORMULA OF CARBOHYDRATES
		D-glyceraldehyde or R-(+)-Glyceraldehyde (CHOCHOHCH2OH)
		D-Glucose and D-Fructose
	CYCLIC STRUCTURE OF MONOSACCHARIDES
	PYRANOSE AND FURANOSE STRUCTURE
		Structure of D-Fructose
	HAWORTH PROJECTION FORMULA
	ANOMERS AND MUTAROTATION
		Structure of few monosaccharides
		GLUCOSE (Dextrose or Grape Sugar or Blood Sugar)
		Chemical Properties of Glucose (Tautomerization):
		Formation of Glycosides
		Oxidation Reaction
	DISACCHARIDES (SUCROSE, MALTOSE AND LACTOSE)
		Sucrose (table sugar, cane sugar, beet sugar):
		Biological Importance
		Inversion of Cane Sugar
		Structure of Sucrose
		Maltose (malt sugar):
		Biological Importance
		Structure
			Lactose
			Occurrence
		Biological Importance
		POLYSACCHARIDES (Starch, glycogen, and cellulose)
		Starch (Homopolysaccharides from D-Glucose)
		Occurrence
		Biological Importance
		Structure
		Amylose
		Amylopectin
		Glycogen
		Structure
		Cellulose
		Structure
	AMINO ACIDS
		Optical Isomerism in Amino Acid
		Classification of Amino Acids
		Non-polar Amino Acids having Hydrophobic R-groups
		Polar Amino Acids with no Change on R-group
		Polar Amino Acids with a Positive Charge on R-group
		Polar Amino Acids with Negative R-group
		Classification of Amino Acids Based on Nutritional Requirement
		Chemical Properties
		Reaction Due to –COOH Group
		Reaction due to –NH2 group
	PROTEINS
		Structure of proteins
		Primary structure
		β-pleated Sheet
		Tertiary Structure of Protein
		Quaternary Structure of Protein
		Properties of Proteins
		Colour Reactions
			Xanthoprotic Test
			Biuret Test
		Millon's Reaction
		Ninhydrin Reaction
		Classification of Protein
		Based on Biological Function
		Simple Proteins
	NUCLEIC ACIDS
		Primary Structure
		Bonding and Nomenclature of Nucleotides and Nucleosides
		Nucleoside di- and tri-phosphate
		Structure of polynucleotide (nucleic acid)
		Secondary Structure
		Tertiary Structure
		Quaternary Structure
		Structure of RNA
	LIPIDS
		Classification of Lipids
		Derived Lipids
		Nomenclature of Fatty Acids
		Abbreviation of Nomenclature of Fatty Acids
		Triacylglycerols (Triglycerides)
		Structure of Acylglycerols
		Properties of Triacylglycerols
		Phospholipids
		Cholesterol
		Brassinosteroids
		Terpenes
		Carotenoids
		Chlorophyll
	BIO-MEMBRANES
		Composition
		Functions
	KEYWORDS
		Eukaryotic Cells
		Thylakoid Membrane
		Integral Protein
		Peripheral Protein
		Endocytosis
	SHORT-ANSWER TYPE QUESTION
	LONG-ANSWER TYPE QUESTIONS
	MULTIPLE CHOICE QUESTIONS
	CONSENT FOR PUBLICATION
	CONFLICT OF INTEREST
	ACKNOWLEDGEMENTS
	REFERENCES
Structure and Biological Function of Vitamins
	Nagendra Nath Yadav1, Archana Pareek1,* and Sonam Tashi Khom1
	INTRODUCTION
	HISTORY
	CLASSIFICATION
	VITAMIN A
		Sources of Vitamin A
		Deficiencies of Vitamin A
		Health Benefits of Vitamin A
		Side Effects due to Excess of Vitamin A
	VITAMIN D
		Sources of Vitamin D
		Deficiencies of Vitamin D
		Health Benefits of Vitamin D
		Side Effects due to Excess of Vitamin D
	VITAMIN E
	SOURCES OF VITAMIN E
		Deficiencies of Vitamin E
		Health Benefits of Vitamin E
		Side Effects due to Excess of Vitamin E
	VITAMIN K
		Sources of Vitamin K
		Deficiencies of Vitamin K
		Health Benefits of Vitamin K
		Side Effects due to Excess of Vitamin K
	VITAMIN C
		Sources of Vitamin C
		Deficiencies of Vitamin C
		Health Benefits of Vitamin C
		Side Effects due to Excess of Vitamin C
	VITAMIN B-COMPLEX
	VITAMIN B1
		Sources of Vitamin B1
		Deficiencies of Vitamin B1
		Health Benefits of Vitamin B1
		Side Effects Due to Excess Vitamin B1
	VITAMIN B2
		Sources of Vitamin B2
		Deficiencies of Vitamin B2
		Health Benefits of Vitamin B2
		Side Effects due to Excess of Vitamin B2
	VITAMIN B3
		Sources of Vitamin B3
		Deficiencies of Vitamin B3
		Health Benefits of Vitamin B3
		Side Effects Due to Excess of Vitamin B3
	VITAMIN B5
		Sources of Vitamin B5
		Deficiencies of Vitamin B5
		Health Benefits of Vitamin B5
		Side Effects Due to Excess of Vitamin B5
	VITAMIN B6
		Sources of Vitamin B6
		Deficiencies of Vitamin B6
		Health Benefits of Vitamin B6
		Side Effects Due to Excess Vitamin B6
	VITAMIN B7
		Sources of Vitamin B7
		Deficiencies of Vitamin B7
		Health Benefits of Vitamin B7
		Side Effects Due to Excess Vitamin B7
	VITAMIN B9
		Sources of Vitamin B9
		Deficiencies of Vitamin B9
		Health Benefits of Vitamin B9
		Side Effects Due to Excess Vitamin B9
	VITAMIN B12
		Sources of Vitamin B12
		Deficiency of Vitamin B12
		Health Benefits of Vitamin B12
		Side Effects Due to Excess Vitamin B12
	KEYWORDS
		Prosthetic Group
		Collagen
		Polyneuritis
		Multiple Sclerosis
		Ataxia
		Skeletal Myopathy
		Retinopathy
		Bulimia
		Korsakoff’s Syndrome
		Leigh’s Disease
		Maple Serum Urine Disease
		Keratoconus
		Glaucoma
		Hartnup Disease
		Megaloblastic Anemia
	VERY SHORT ANSWER TYPE QUESTION
	SHORT-ANSWER TYPE QUESTIONS
	LONG-ANSWER TYPE QUESTIONS
	MULTIPLE CHOICE QUESTIONS
	CONSENT FOR PUBLICATION
	CONFLICT OF INTEREST
	ACKNOWLEDGEMENTS
	REFERENCES
Enzymes (Biocatalyst)
	Nagendra Nath Yadav1,*, Archana Pareek1 and Kamlesh Singh Yadav2
	INTRODUCTION
	ENZYME STRUCTURE
	NOMENCLATURE AND CLASSIFICATION
		Recommended Name
		Systematic Name
	FACTORS AFFECTING ENZYME ACTIVITY
		Concentration of Enzyme
		Substrate Concentration
		Effect of Temperature
		Temperature of Coefficient (Q10)
		Effect of pH
		Effect of the Concentration of Product
	ENZYME KINETICS
		Mechanism of Enzyme Action
		Enzyme-substrate Complex Formation
			Fisher’s Lock and Key Model or Fisher’s Template Theory
			Koshland’s Induced Fit Model
	ENZYME INHIBITION
		Reversible Inhibition
		Competitive Inhibition
			Non-competitive Inhibition
		Irreversible Inhibition
	PHYSICO-CHEMICAL NATURE OF ENZYME
	CHARACTERISTICS OF ENZYMES
	COENZYMES
	BIOLOGICAL FUNCTIONS OF COENZYME
		Adenosine triphosphate (ATP)
		Thymine Pyrophosphate (TPP)
		Flavin mononucleotide (FMN)
		Nicotinamide adenine dinucleotide (NAD  +  )
		Biocytin
	CONTROL ACTIVITY OF ENZYMES
		Regulation
		Post-translational Modification (PTM)
		Quantity
		Subcellular Distribution
		Organ Specialization
	KEYWORDS
		Catalyst
		Dialysis
		Denaturation
		Biological Catalyst
	SHORT-ANSWER TYPE QUESTIONS
	LONG-ANSWER TYPE QUESTIONS
	MULTIPLE CHOICE QUESTIONS
	CONSENT FOR PUBLICATION
	CONFLICT OF INTEREST
	ACKNOWLEDGEMENTS
	REFERENCES
Hormones
	Nagendra Nath Yadav1,* and Archana Pareek1
	INTRODUCTION
	CLASSIFICATION OF HORMONES
		According to the Chemical Nature
		On the Basis of the Mechanism of Action
		According to the Nature of the Action
		According to the Effect
		On the Basis of Stimulation of Endocrine Glands
		Adrenocorticotropic Hormones (ACTH)
		Thyroid-Stimulating Hormone (TSH)
		Growth Hormones (GH)
		Oxytocin
		Vasopressin
		Aldosterone
		Adrenaline
		Noradrenaline
		Estrogen
		Progesterone
		Testosterone
		Luteinizing Hormone (LH)
		Follicle-stimulating Hormone (FSH)
		Prolactin (PRL)
	REGULATION OF HORMONES
	HORMONES IN PLANTS
		Type of Plant Hormones
			Auxins
			Cytokinins
			Gibberellins
			Ethylene
			Abscisic Acid
	HORMONES IN INSECTS
		Brain Hormones
		Molting Hormones
		Juvenile Hormones
	KEYWORDS
		T-cells
		Glucogenesis
		Glycoprotein
		Addison’s Disease
		Osteoporosis
		Tonicity
		Rosette Plant
	SHORT-ANSWER QUESTIONS
	LONG-ANSWER TYPE QUESTIONS
	MULTIPLE CHOICE QUESTIONS
	CONSENT FOR PUBLICATION
	CONFLICT OF INTEREST
	ACKNOWLEDGEMENTS
	REFERENCES
Fundamentals of Thermodynamics: Principle Applicable To Biological Processes
	Nene Takio1,*, Pratibha Yadav2 and Anindita Hazarika1
	INTRODUCTION
		What is the Basic Concept of Thermodynamics?
	STATE VARIABLES
	ENERGY TRANSFER INTO HEAT & WORK
	THE FIRST LAW: LAW OF CONSERVATION OF TOTAL ENERGY
	ENTHALPY IS A USEFUL FEATURE FOR BIOLOGICAL SYSTEMS
	THE SECOND LAW: SYSTEM TENDS TOWARD DISORDER AND RANDOMNESS
		Attributes of the Entropy Function
	THE THIRD LAW: ENTROPY CHANGE AT ABSOLUTE ZERO
	GIBBS FREE ENERGY
	THE STANDARD STATE FREE ENERGY CHANGE
	EXAMPLE:
	THERMODYNAMIC PARAMETERS AFFECTING BIOCHEMICAL EVENTS
	EFFECT OF PH ON STANDARD FREE ENERGIES CHANGE
	REACTION OF CONCENTRATION AND FREE ENERGY CHANGE
	COUPLED PROCESS
	ATP (ADENOSINE TRIPHOSPHATE)
	THERMODYNAMIC HYDROLYSIS OF ATP
		Structure of ATP
	FACTORS AFFECTING HYDROLYSIS OF FREE ENERGY OF ATP
	HYDROLYSIS OF ATP AND EQUILIBRIA OF COUPLED REACTIONS
	DAILY HUMAN REQUIREMENT FOR ATP
	SUMMARY
	KEYWORDS
		Pyruvate
		Denaturation
		Calorimeter
		Glycolysis
		Phototrophs
	SHORT-ANSWER TYPE QUESTION
	MULTIPLE CHOICE QUESTIONS
	CONSENT FOR PUBLICATION
	CONFLICT OF INTEREST
	ACKNOWLEDGEMENTS
	REFERENCES
Bioenergetics, Metabolism of Biomolecules, Photosynthesis and Respiration, Transcription and Translation, Recombinant DNA Technology
	Saroj Yadav1,*, Kamlesh Singh Yadav2 and Pratibha Yadav3
	INTRODUCTION
	BIOENERGETICS
		Theory of Bioenergetics
		Laws of Thermodynamics in Bioenergetics
		Equilibrium Constant and Free Energy
		Endergonic and Exergonic Reactions
			Exergonic Reactions
			Endergonic Reactions
		Activation Energy
		Coupled Reaction in Bioenergetics
	METABOLISM OF CARBOHYDRATES
		Glycolysis
		Classification of Glycolysis
		Glycolysis Pathway in Steps
		Glucose Activation Phase
		Step-1
		Step-2
		Step-3
		Step-4
		Step-5
		Payoff Phase
		Step-6
		Step-7
		Step-8
		Step-9
		Anaerobic Condition
		Significance of the Glycolysis Pathway
	LIPIDS METABOLISM
		Biosynthesis of Lipid
		Degradation of Lipid
	METABOLISMS OF PROTEINS
		Protein Synthesis
		Chemical Synthesis of Protein
		Protein Degradation
	METABOLISM OF NUCLEIC ACID
		Synthesis of Nucleic Acids
		Decomposition of Nucleic Acid (DNA and RNA)
		Catabolism of Pyrimidine
		Purine Catabolism
	PHOTOSYNTHESIS AND RESPIRATION
		Similarities between Photosynthesis and Respiration
	OXIDATIVE PHOSPHORYLATION
		Electron Transport and Synthesis of ATP
	DNA REPLICATION
	TRANSCRIPTION
		Formation of pre-mRNA
	TRANSLATION
		Transfer RNA
		Protein Synthesis
	RECOMBINANT DNA TECHNOLOGY
		Instruments for Recombinant DNA Innovation:
		Recombinant DNA Technology Steps
		Application of Recombinant DNA Technology
	SUMMARY
	KEYWORDS
		Glycolysis
		The Cycle of Citric Acid
		Ketosis
		Oxidative Phosphorylation
		Photosynthesis
		Catabolism
		Photorespiration
		Recombinant DNA
	LONG QUESTIONS
	SHORT-QUESTIONS
	MULTIPLE CHOICE QUESTIONS
	CONSENT FOR PUBLICATION
	CONFLICT OF INTEREST
	ACKNOWLEDGEMENTS
	REFERENCES
Subject Index
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