Genetics Fundamentals Notes

Contents
About the Editors
Part I: Classical Genetics
1: Fundamentals of Genetics
1.1 From Mendel Theory to Discovery of DNA
1.1.1 Mendel´s Work
1.1.2 Mendelian Theory of Inheritance
1.1.3 Genetic Variation
1.2 Model Organisms
1.2.1 Escherichia coli
1.2.2 Saccharomyces cerevisiae
1.2.3 Drosophila melanogaster
1.2.4 Arabidopsis thaliana
1.2.5 Mus musculus
1.3 Genetics and Evolution
1.3.1 Natural Selection
1.3.2 Evolutionary Lineage
1.4 Genetics in Biological Research
1.4.1 Forward Genetics
1.4.2 Reverse Genetics
1.4.3 Manipulation of DNA
1.5 Pathway of Genetic Analysis
1.5.1 Classical Genetics
1.5.2 Molecular Genetics
1.5.3 Population Genetics
1.6 Genetic Database
1.7 Application of Genetics
1.8 Promise of Genetics
Box 1.1 Scientific Concept: Forward and Reverse Genetic Approaches for the Analysis of Vertebrate Development in the Zebrafish...
1.9 Summary
References
2: Mendelian Principle of Inheritance
2.1 Mendelian´s Monohybrid Cross
2.1.1 The Garden Pea
2.1.2 Concept of Dominant and Recessive Traits
2.1.3 Segregation of Alleles
2.1.4 Mendel´s Analytic Approach
2.1.5 Test Cross: One Character
2.2 Mendelian Dihybrid Cross
2.2.1 Independent Assortment
2.2.2 Test Cross: Two Characters
2.3 Mendelian Trihybrid Cross
2.4 Application of Mendelian Principles
2.4.1 The Punnett Square Method
2.4.2 The Forked Line Method
2.4.3 The Probability Method
2.4.3.1 Binomial Theorem
2.5 Test of Genetic Hypothesis
2.5.1 The Chi-Square Test
2.6 Application of Mendelian Principles in Human Genetics
2.6.1 Pedigree Analysis
2.6.2 Mendelian Segregation
2.6.3 Genetic Counselling
Box 2.1 Scientific Concept: Gregor Mendel´s Genetic Experiments: A Statistical Analysis After 150 Years (Jan Kalina)
2.7 Summary
References
3: Extension of Mendelism
3.1 Multiple Alleles
3.1.1 ABO Blood Groups
3.1.2 The A and B Antigens
3.1.2.1 Biochemistry of ABO Blood Antigens
3.1.3 The Bombay Phenotype
3.1.3.1 Biochemistry of H Antigen
3.1.3.2 Clinical Significance of Anti-H Antibodies
3.1.3.2.1 Transfusion Reactions
3.1.3.2.2 Hemolytic Disease of the Newborn (HDN)
3.1.4 Drosophila Eye Color
3.2 Dominance Relationship
3.2.1 Dominance
3.2.2 Incomplete Dominance
3.2.2.1 Incomplete Dominance in Fruit Color of Eggplants
3.2.2.2 Incomplete Dominance in Feather Color in Chicken
3.2.2.3 Incomplete Dominance in Skin Pattern of Horses
3.2.2.4 Mechanism of Incomplete Dominance
3.2.2.5 Examples of Incomplete Dominance in Humans
3.2.3 Complexities Involved in the Concept of Dominance
3.2.4 Codominance
3.2.4.1 Codominance in Human Blood Groups
3.2.5 Lethal Alleles
3.2.6 Sex-Limited Traits
3.2.7 Sex-Influenced Traits
3.3 X-Linkage Feature Genes
3.3.1 X-Linkage in Drosophila
3.3.2 X-Linkage in Humans
3.3.2.1 X-Linked Blood-Clotting Disorder: Hemophilia
3.3.2.2 X-Linked Vision Disorder: Color Blindness
3.4 Genotype to Phenotype
3.4.1 Penetrance
3.4.2 Expressivity
3.4.3 Environmental Effects on Gene Expression
3.4.3.1 Position Effect
3.4.3.2 Temperature Effect
3.4.3.3 Nutritional Effect
3.4.3.4 Pleiotropy
3.4.4 Gene Interaction
3.4.4.1 Production of Novel Phenotypes by Gene Interaction
3.4.4.2 Epistasis
3.4.4.3 Recessive Epistasis
3.4.4.4 Dominant Epistasis
3.4.4.5 Duplicate Gene Interaction
3.4.4.5.1 Duplicate Recessive Epistasis
Flower Color in Peas
Albinism in Freshwater Snail Physa heterostropha
3.4.4.5.2 Duplicate Dominant Epistasis
Wheat Kernel Color
Box 3.1 Scientific Concept: Epistasis and Disease
Box 3.2 Scientific Concept: Diseases with Complex Inheritance Patterns
3.5 Extranuclear Inheritance
3.5.1 Extranuclear Genomes: Mitochondria
3.5.2 Extranuclear Genomes: Chloroplast
3.5.3 Experimental Methods to Deduce Extranuclear Inheritance
3.5.4 Extranuclear Inheritance: Examples
3.5.4.1 Maternal Effects
3.5.4.1.1 Snail Coiling
3.5.4.1.2 Moth Pigmentation
3.5.4.2 Mitochondria-Mediated Inheritance
3.5.4.2.1 Poky Strain in Neurospora
3.5.4.2.2 Petites in Yeast
3.5.4.2.3 Human Mitochondrial Inheritance
3.5.4.2.4 Mitochondrial Inheritance in Yeast: Antibiotic Influences
3.5.4.3 Chloroplast-Mediated Inheritance
3.5.4.3.1 Variegation in Zea mays
3.5.4.3.2 Variegation in Four O´clocks
3.5.4.3.3 Antibiotic Resistance in Chlamydomonas
3.5.4.4 Infective Particles
3.5.4.4.1 Paramecium
3.5.4.4.2 Kappa Particles and Killer Paramecium
3.5.4.4.3 Mate-Killer Infection and Mu Particles
3.5.4.4.4 Sex-Ratio Phenotype in Drosophila
Box 3.3 Scientific Concept: Evolution of Approaches to Study Complex Diseases and Mapping of Gene Interactions (GIs)
Box 3.4 Scientific Concept: GI and Cancer
3.6 Summary
4: Chromosome Mapping in Eukaryotes
4.1 Linkage, Recombination, and Crossing over
4.1.1 Determination of Linkage
4.1.1.1 Coupling and Repulsion Hypothesis
4.1.1.2 Coupling and Repulsion Explained
4.1.1.3 Mechanism of Crossing over and Recombination
4.1.2 Proof That Crossing over Makes Recombination
4.1.3 Chiasmata and Crossing over
4.1.4 Sturtevant and Mapping
4.1.5 Linkage Analysis
4.1.5.1 Linkage Analysis with Different Types of Organisms Can Be Categorized as Follows
4.2 Gene Mapping with Recombination Frequencies, Calculation of Map Distance, and Concept of Map Units
4.2.1 Gene Mapping Through Two-Point Test Cross
4.2.2 Gene Mapping Through Three-Point Test Cross
4.2.2.1 Determining Gene Order
4.2.2.2 Determining Distance Between Genes
4.2.2.3 Interference and the Coefficient of Coincidence
4.2.3 Mapping in Neurospora and Yeast: Haploid Mapping (Tetrad Analysis)
4.2.3.1 Phenotypes of Fungi
4.2.3.2 Identification of Linkage and Mapping Genes in Yeast by Analysis of Unordered Spores
4.2.3.2.1 Mapping in Neurospora
4.2.3.2.2 First- and Second-Division Segregation
4.2.3.3 Gene Order Determination
4.2.3.4 Mapping of Centromere Using Linear Tetrads
4.3 Construction of Genetic Maps of Human Genome
4.3.1 Mapping by Pedigree Analysis: X-Linkage
4.3.2 Mapping by Pedigree Analysis: Autosomal Linkage
4.3.3 Using Lod Score Method to Assess Linkage in Human Pedigrees
4.3.4 Assigning Genetic Loci to Chromosomes
4.3.4.1 Chromosomal Banding
4.3.4.1.1 ISCN Mapping System
4.3.4.2 Somatic Cell Hybridization
4.3.5 Chi-Square Test in Linkage Analysis
4.4 Comparison of Genetic Map and Physical Map
4.4.1 Genetic Mapping
4.4.2 DNA Markers for Genetic Mapping
4.4.2.1 RFLPs (Restriction Fragment Length Polymorphisms)
4.4.2.2 SSLPs (Simple Sequence Length Polymorphisms)
4.4.2.3 SNP (Single Nucleotide Polymorphism)
4.4.3 Physical Mapping
4.4.3.1 Restriction Mapping
4.4.3.1.1 Basic Methodology Involved in Restriction Mapping
4.4.3.1.2 Examining DNA Molecules Directly for Restriction Sites
4.4.3.2 FISH (Fluorescence In Situ Hybridization)
4.4.3.3 STS (Sequence-Tagged Site) Mapping
4.4.3.4 Genetic Distance vs Physical Distance
Box 4.1 Scientific Concept: Estimation of Distances and Map Construction Using Radiation Hybrids: William Newell
4.5 Summary
References
5: Study of Chromosome
5.1 Overview of Chromosome
5.1.1 Chromosome Number
5.1.2 Autosome
5.1.3 Sex Chromosome
5.2 Chromosomal Basis of Heredity
5.2.1 Proof That Inheritance Linked to Chromosome
5.2.2 Nondisjunction: Proof of Chromosome Theory
5.2.3 Chromosomal Basis of Mendelian Theory
5.3 Sex-Linked Genes: Human
5.3.1 Haemophilia: X-Linked
5.3.2 Colour Blindness: X-Linked
5.3.2.1 X-Linked Dominant Disorders
5.3.2.2 Rett Syndrome
5.3.2.3 Fragile X Syndrome
5.3.3 Genes on Y Chromosome
5.3.4 Genes Both on X and Y Chromosomes
5.4 Concept of Sex Determination
5.4.1 Y Chromosome: Maleness
5.4.1.1 Klinefelter Syndrome
5.4.1.2 Turner Syndrome
5.5 Analysis of Sex-Linked Traits
5.5.1 X-Linked Recessive Inheritance
5.5.2 X-Linked Dominant Inheritance
5.5.3 Y-Linked Inheritance
5.6 Techniques for Studying Chromosome
5.6.1 Cytological Fixatives
5.6.1.1 Mercuric Chloride (HgCl2)
5.6.1.2 Potassium Dichromate (k2Cr2O7)
5.6.1.3 Chromic Acid (H2CrO4) or Chromium Trioxide (CrO3)
5.6.1.4 Osmium Tetroxide (OsO4)
5.6.1.5 Ethanol (C2H5OH)
5.6.1.6 Acetic Acid (CH3COOH)
5.6.1.7 Formaldehyde (HCHO)
5.6.1.8 Propionic Acid (C2H5COOH)
5.6.1.9 Chloroform (CHCl3)
5.6.1.10 Fixing Mixtures
5.6.1.11 Flemming´s Weak Fluid (1882) and Flemming´s Strong Fluid (1884) (Table 5.3)
5.6.1.12 Carnoy´s Fluid (1886) or Carnoy´s Fixative 1 (Table 5.4)
5.6.1.13 Carnoy´s Fluid II (1886) (Table 5.5)
5.6.1.14 Navaschin´s Fluid (Navaschin 1925) (Table 5.6)
5.6.2 Cytological Stains
5.6.2.1 Carmine
5.6.2.2 Orcein
5.6.2.3 Crystal Violet
5.6.2.4 Acetocarmine, Aceto-orcein (Table 5.7)
5.6.2.5 Crystal Violet
5.6.2.6 Schiff´s Reagent/Fuchsine Reagent (Table 5.8)
5.6.3 Cytological Pretreating Agents
5.6.3.1 Colchicine
5.6.3.2 α-Bromonaphthalene
5.6.3.3 8-Hydroxyquinoline
5.6.3.4 p-Dichlorobenzene (p-DCB)
5.6.4 Analysis of Mitotic Chromosome
5.6.4.1 Prophase
5.6.4.2 Prometaphase
5.6.4.3 Metaphase
5.6.4.4 Anaphase
5.6.4.5 Telophase and Cytokinesis
5.6.5 Analysis of Human Karyotype
5.6.6 Cytological Variation
5.7 Monosomy: Cri-du-Chat Syndrome
5.8 Trisomy
5.8.1 Down Syndrome
5.8.2 Patau Syndrome
5.8.3 Edwards Syndrome
5.9 Polyploidy
5.9.1 Autopolyploidy
5.9.2 Allopolyploidy
5.9.3 Endopolyploidy
5.10 Chromosome Shuffling
5.10.1 Deletions
5.10.2 Duplications
5.10.3 Inversion
5.10.4 Translocation
5.11 Fragile Site: Chromosomal Breakage
Box 5.1
5.12 Summary
References
6: Genetic Study of Bacteria and Bacteriophage
6.1 Bacterial Genetics
6.1.1 Bacterial Mutant Genetics
6.1.1.1 Mutant Detection
6.1.1.2 Mutant Selection
6.1.2 Spontaneous Mutation in Bacteria
6.2 Viral Genetics
6.2.1 Structure of Bacteriophage T4
6.2.1.1 DNA Packaging
6.2.2 Life Cycle of Bacteriophage T4
6.2.3 The Plaque Assay
6.2.4 Lysogeny
6.2.5 T4 Phage Modulates Bacterial Genetics
6.2.5.1 Human Gut Microbiome Interaction
6.2.5.2 Host Communication
6.2.5.3 Host Replication
6.2.5.4 Host Metabolism and Energy
6.2.6 CRISPR/Cas9 Bacteria in Genetic Engineering
6.2.7 Application of CRISPR/Cas9
6.3 Conjugation
6.3.1 Discovery of Conjugation
6.3.2 Discovery of Fertility Factor (F)
6.3.3 F+ and F- Bacteria
6.3.4 Hfr Bacteria
6.3.5 Mapping of Bacterial Chromosome
6.3.6 F+xF- Mating
6.3.7 F Plasmid
6.3.8 R Plasmid
6.4 Transformation
6.4.1 Discovery of Transformation
6.4.2 Transformation Process
6.4.3 Transformation Linked Genes
6.5 Transduction
6.5.1 Discovery of Transduction
6.5.2 Generalized Transduction
6.5.3 Specialized Transduction
6.5.4 Lambda (lambda) Genetics
6.5.5 Nature of Transduction
6.6 Infectious (Bacterial/Viral) Disease
6.6.1 SARS-CoV
6.6.2 MERS-CoV
6.6.3 COVID-19
Box 6.1 Scientific Concept: Genetic Exchange Between Escherichia coli Strains in the Mouse Intestine-Jones R T et al.
Box 6.2 Scientific Concept: Role of Pili in Bacterial Conjugation-Ou, J. T et al.
6.7 Summary
References
Part II: Molecular Genetics I: Analysis of Gene
7: Replication of DNA
7.1 Classical Experiments: DNA as Genetic Material
7.1.1 Transformation: Early Study
7.1.2 Avery, MacLeod and McCarty´s Experiment
7.1.3 Hershey and Chase Experiment
7.1.4 Transfection Study
7.2 Molecular Evidence: DNA as Genetic Material
7.2.1 Indirect Evidence: DNA Distribution
7.2.2 Indirect Evidence: DNA Mutagenesis
7.2.3 Direct Evidence: rDNA Study
7.2.4 RNA Serves as Genetic Material
7.2.4.1 RNA as the Genetic Material in Viruses
7.3 Structure of DNA Helix
7.3.1 Base Composition Study
7.3.2 X-Ray Diffraction Study
7.3.3 Watson and Crick´s Model
7.3.3.1 Triplex DNA
7.3.3.2 Alternative Forms of DNA
7.4 Analytical Study on DNA and RNA
7.4.1 Absorption of UV Light
7.4.2 Sedimentation Velocity Centrifugation
7.4.3 Denaturation and Renaturation of Nucleic Acids
7.4.4 Hypochromic Effect
7.4.5 FISH
7.4.6 DNA Renaturation Kinetics
7.4.7 Repetitive DNA
7.4.8 Electrophoresis of Nucleic Acids
7.4.8.1 Pulse Field Gel Electrophoresis
7.5 DNA Replication: Semi-conservative
7.6 Different Modes of DNA Replication
7.7 Mechanism of DNA Polymerase
7.8 Process of DNA Replication
7.8.1 DNA Replication at the Replication Fork
7.8.2 Unwinding of Double Helix
7.8.3 Synthesis of RNA Primer
7.8.4 Synthesis of DNA by DNA Polymerase
7.8.5 Synthesis of Leading and Lagging Strand
7.8.6 Formation of DNA Replication Complex
7.9 Mechanism of DNA Ligase
7.10 Prokaryotic vs Eukaryotic DNA Replication
7.10.1 Eukaryotes Have Many Different DNA Polymerases
7.10.2 Removal of RNA Primers
7.10.3 End Replication Problem
7.10.4 Role of Telomeres in Cancer and Ageing
7.11 Regulation of DNA Replication
Box 7.1 Scientific Concept: Using Amino-Labelled Nucleotide Probes for Simultaneous Single Molecule RNA-DNA FISH, Reelina Basu...
Box 7.2 DNA Mutation Motifs in the Genes Associated with Inherited Diseases, Michal Ruzicka et al.
7.12 Summary
References
8: Chromosomal Organization of DNA
8.1 Chromosome: Overview
8.2 DNA Supercoiling
8.3 Organization of the Prokaryotic Chromosome
8.4 Hierarchical Packaging of the Eukaryotic Chromosome
8.4.1 The Nucleosome Assembly
8.4.2 The Solenoid Structure
8.4.3 The Chromosomal Structure
8.5 The Heterochromatin and Euchromatin
8.6 Chromosomal Banding
8.7 Morphology of the Eukaryotic Chromosome
8.7.1 The Centromere
8.7.2 The Secondary Constriction
8.7.3 Satellite DNA
8.7.4 The Telomere
8.8 Specialized Chromosomes
8.8.1 The Polytene Chromosome
8.8.2 Lampbrush Chromosome
Box 8.1 Scientific Concept: Investigating DNA Supercoiling in Eukaryotic Genomes: Samuel Corless and Nick Gilbert
8.9 Chapter Summary
Further Reading
9: DNA Mutation, Repair, and Recombination
9.1 Mutation: Overview of the Process
9.1.1 A Different Class of Mutation
9.1.2 Parameter 1: Size of the Affected DNA
9.1.3 Parameter 2: Mode of Occurrence
9.1.4 Parameter 3: Target Cell Type
9.1.5 Parameter 4: Impact of Translated Peptide
9.1.6 Frameshift and In-Frame Mutation
9.1.7 Synonymous and Non-synonymous Base Substitution
9.1.8 Parameter 3: Character of Base Alteration
9.1.9 An Outline of Transition-Transversion Bias
9.1.10 Similarity and Contrast: Synonymous Substitution Mutations, Silent Mutation, and Neutral Mutation
9.1.11 Mutations Affect Gene Expression: ``Loss of Function´´ Versus ``Gain of Function´´
9.1.12 Mutations Are Instrumental in Evolution: ``Gradual Change´´ Versus ``Quick Jump´´
9.1.13 Mutation Rate
9.1.14 Mutation Hotspot
9.1.15 Somatic and Germinal Mutation
9.1.16 Spontaneous or Induced Mutation
9.1.16.1 Spontaneous Mutation
9.1.16.2 Depurination
9.1.16.3 Deamination
9.1.17 Mutation: A Reverse Phenomenon
9.1.17.1 Reverse Mutations and Suppressor Mutations
9.1.18 Mutagenesis in Bacteria
9.2 Mutation: Phenotypic Effects
9.2.1 Phenotypic Effects
9.2.2 Inheritance of Mutation
9.2.3 Morgan´s Experiment
9.3 Mutation: Mechanism
9.3.1 Induced Mutation
9.3.2 Induced by Radiation
9.3.3 Induced by Chemical
9.3.3.1 Incorporation of Base Analogs
9.3.3.2 Specific Mispairing by Alkylating Agents
9.3.3.3 DNA Intercalating Agents
9.3.3.4 DNA Cross-Linkers
9.3.3.5 Aflatoxin B1
9.3.4 Induced by Transposable Elements
9.3.4.1 Tn5 Transposon
9.3.4.2 ``Sleeping Beauty´´ Transposon
9.3.5 Trinucleotide Repeat: Mutation
9.3.5.1 CAG Repeats
9.3.5.2 Why `Three´ No Other Numbers in Nucleotide Repeats
9.3.5.3 The Practical Implication of Mutagenesis: Site-Directed Mutagenesis
9.4 Test for Mutagenicity: The Ames Test
9.5 DNA Repair Mechanism
9.5.1 An Overview of a Global Response to DNA Damage
9.5.2 Light-Dependent Repair
9.5.3 Base Excision Repair
9.5.3.1 Short-Patch BER and Long-Patch BER
9.5.4 Mismatch Repair
9.5.5 Nucleotide Excision Repair
9.5.6 Other Types of DNA Repair System
9.5.7 Pathological Impact of Impaired DNA Repair Mechanism
9.6 Mechanism of DNA Recombination
9.7 Types of DNA Recombination
9.8 Models of DNA Recombination
Box 9.1 Scientific Concept: Testing the Mutagenicity Potential of Chemicals: Geert R Verheyen et al.
9.9 Conclusion
9.10 RuvC Enzyme and Holliday Junction
9.11 Summary
References
10: RNA Transcription
10.1 RNA Transcription: Overview
10.2 Types of RNA: Overview
10.3 Process of RNA Transcription
10.3.1 Prokaryotes
10.3.2 Promoter Recognition by RNA Polymerase
10.3.3 Eukaryotes
10.3.4 Initiation of Transcription in Eukaryotes
10.3.5 Transcription Through Nucleosomes
10.3.6 Elongation
10.3.7 Termination
10.4 RNA Polymerase: Mechanism
10.4.1 The Three Eukaryotic RNA Polymerases (RNAPs)
10.5 Prokaryotic vs Eukaryotic RNA Transcription
10.6 Regulation of RNA Transcription
10.6.1 Repression of Transcription Initiation
10.6.2 Small RNAs
10.6.3 Regulation of Transcription Initiation via Changes in DNA Topology
10.7 RNA Processing: Mechanism
10.7.1 Processing of mRNA
10.7.1.1 5′ Capping
10.7.1.2 3′ Polyadenylation
10.7.1.3 RNA Splicing
10.7.1.4 Alternative Splicing
10.7.1.5 Sequestration as RNP
10.7.2 Processing of tRNA
10.7.2.1 Secondary and Three-Dimensional Structure of tRNA
10.7.3 Processing of rRNA
10.8 RNA Editing: Mechanism
10.8.1 A-to-I Editing
10.8.2 C-to-U Editing
10.8.3 Editing in Mitochondria
10.8.3.1 Types of RNA Editing in Mitochondria
10.8.4 Editing in Plastid
10.8.5 Coediting in Virus
Box 10.1 Scientific Concept: High-Throughput Detection of RNA Processing in Bacteria: Erin E. Gill et al.
10.9 Summary
References
11: Protein Translation
11.1 Genetic Code
11.1.1 Non-overlapping Nature of the Code
11.1.2 Degenerate Nature of Code
11.1.3 Deciphering Genetic Code
11.1.4 Synthesizing Polypeptides in a Cell-Free System
11.2 Codon: tRNA Interaction
11.3 Structure of Ribosome
11.4 Structure of tRNA
11.5 Charging of tRNA
11.6 Proofreading Activity of Protein and Its Comparison to RNA and DNA Synthesis
11.7 Process of Protein Translation
11.7.1 Initiation
11.7.2 Elongation
11.7.3 Termination
11.7.4 Polyribosome
11.7.5 Translation of Polycistronic mRNA
11.8 Prokaryotic vs Eukaryotic Protein Translation
11.8.1 Eukaryotic Translation Initiation
11.8.1.1 5′ mRNA Capping
11.8.1.2 Circularization of mRNA During Translation
11.8.1.3 Eukaryotic Translation Elongation
11.8.1.4 Eukaryotic Translation Termination
11.9 Regulation of Protein Translation
11.9.1 Translation Pause
Box 11.1 Scientific Concept: Protein Synthesis by Single Ribosomes: Francesco Vanzi et al.
Box 11.2 Scientific Concept: Errors in Protein Synthesis Increase the Level of Saturated Fatty Acids and Affect the Overall Li...
Box 11.3 Scientific Concept: Protein Synthesis by Single Ribosomes: Francesco Vanzi et al.
11.10 Summary
References
12: Regulation of Gene Expression in Prokaryotes
12.1 Concept of Gene Regulation
12.2 Concept of Operon
12.3 Metabolism of Lactose in E. coli
12.3.1 Lactose Uptake in E. coli
12.3.2 Structural Gene
12.3.3 Regulatory Mutation
12.3.4 Positive and Negative Control
12.3.5 Genetic Evidence for Operon Model
12.4 Mechanism of Lac Operon
12.5 Regulation of Lac Operon
12.6 Effect of Mutation on Lac Operon
12.7 Trp Operon in E. coli
12.7.1 Trp Operon Structural Genes
12.7.2 Concept of Attenuation
12.7.3 Mechanism of Trp Operon
12.8 Regulation of Gene Expression in Lambda Phage
12.8.1 Lysogenic Pathway
12.8.2 Lytic Pathway
Box 12.1: Scientific Concept: Mechanism of Promoter Repression by Lac Repressor-DNA Loops - Nicole A. Becker et al.
12.9 Summary
References
13: Regulation of Gene Expression in Eukaryotes
13.1 Control of Transcription by Protein
13.1.1 By Activators
13.1.2 By Repressors
13.1.3 By Steroid Hormones
13.2 Regulation of Transcription by Chromatin
13.2.1 Chromatin Remodeling
13.2.2 Histone Modification
13.2.2.1 Histone Acetylation
13.2.2.2 Histone Methylation
13.2.2.3 Histone Phosphorylation
13.2.2.4 Histone ADP Ribosylation
13.2.2.5 Histone Sumoylation and Ubiquitylation
13.2.2.6 Other Histone Modifications
13.3 Gene Silencing by DNA Methylation
13.3.1 Mechanism of Gene Silencing by DNA Methylation
13.3.2 DNA Methylation and Its Interaction with Other Chromatin Modifiers
13.3.3 Demethylation of DNA
13.3.4 DNA Methylation and Diseases
13.4 Alternative Splicing of mRNA
13.4.1 Molecular Mechanism of Splicing
13.4.2 Modes of Alternative Splicing
13.4.3 Alternative Splicing and Disease
13.5 RNA Interference
13.5.1 MicroRNA
13.5.2 Small Interfering RNA
13.5.3 Molecular Mechanism of RNA Interference
13.5.4 Applications of RNA Interference
13.6 Posttranscriptional Regulation of Gene Expression
13.6.1 Control of mRNA Degradation
13.6.1.1 3′ Deadenylation
13.6.1.2 Decapping
13.6.1.3 5′ to 3′ mRNA Degradation by Xrn-1 Endonuclease
13.6.1.4 3′ to 5′ Degradation by Exosomes
13.6.1.5 Other Types of Aberrant mRNA Degradation
13.6.2 Control of Protein Degradation
13.6.2.1 Autophagy
13.6.2.2 Ubiquitin-Proteasome Pathway
13.6.2.3 Mechanism of Protein Degradation by Ubiquitin Proteosome
13.6.2.4 Ubiquitination and Diseases
Box 13.1: Scientific Concept: Quantifying Site-Specific Chromatin Mechanics and DNA Damage Response
Box 13.2: Scientific Concept: Transcriptional Gene Silencing in Humans
13.7 Chapter Summary
References
Part III: Molecular Genetics II: Analysis of Genomes
14: Techniques of Molecular Genetics
14.1 Recombinant DNA Technology
14.1.1 Vector-Vehicle of Carrying DNA
14.1.2 Cloning Strategies
14.1.3 Polymeric Chain Reaction (PCR)
14.2 Construction of Library
14.2.1 Construction of Genomic Library
14.2.2 Construction of cDNA library
14.2.3 Construction of Chromosome-Specific Library
14.3 Screening of Gene Library
14.3.1 Hybridization
14.3.2 Colony Hybridization
14.3.3 PCR
14.3.4 Immunological Assay
14.3.5 Protein Function
14.4 Screening of the Genomic Library
14.4.1 Screening by Hybridization
14.4.2 Expression
14.4.2.1 Library Plating
14.4.2.2 Western Blot Analysis
14.4.3 Hybrid Arrest and Release
14.4.3.1 HRT and HART (Hybrid Release Translation and Hybrid Arrest Translation)
14.4.4 Chromosomal Walking
14.5 Site-Directed Mutagenesis by PCR
14.5.1 PCR Method of Site-Directed Mutagenesis
14.5.2 Overlap Extension Method
14.5.3 Megaprimer Method
14.5.4 Inverse PCR-Based Technique
14.6 Visualization of Biomolecules
14.6.1 Visualizing DNA by Southern Blot
14.6.1.1 Procedure of Southern Blotting
14.6.1.2 Applications of Southern Blotting
14.6.2 Visualizing RNA by Nothern Blot
14.6.2.1 Applications of Nothern Blot
14.6.3 Visualizing RNA by RT-PCR
14.6.4 Visualizing Proteins by Western Blotting
14.7 Analyses of Gene
14.7.1 Physical Mapping by Restriction Endonuclease
14.8 Sequencing of Genes
14.8.1 High-Throughput Sequencing (HST)
14.8.1.1 Illumina
14.8.1.2 Life Technologies/ThermoFisher/Ion Torrent
14.8.1.3 Pacific Biosciences
14.8.1.4 Oxford Nanopore Technologies
14.8.2 Whole Genome Sequencing
Box 14.1: Scientific Concept: Efficient Method for Site-Directed Mutagenesis in Large Plasmids Without Subcloning - Louay K. H...
Box 14.2: Scientific Concept: The pPSU Plasmids for Generating DNA Molecular Weight Markers
14.9 Summary
15: Genomics
15.1 Overview of Genomic Analysis
15.1.1 Sequence Compilation
15.1.2 Sequence Annotation
15.2 Functional Genomics
15.3 Features of Prokaryotic Genome
15.3.1 Introduction
15.3.2 Concept and Classification of Replicons
15.3.3 Genomic Signatures of Bacterial Replicons
15.3.3.1 Usage of Codon
15.3.3.2 GC Content
15.3.3.3 Relative Quantity of Dinucleotide
15.3.4 Physical Structure of the Prokaryotic Genome
15.3.5 Repeats in Prokaryotic Genome
15.3.5.1 Recombination and Repeats
15.3.5.2 Origin of Repeats
15.3.5.3 Repeats of Generic Nature
15.3.5.4 Selfish Elements
15.3.5.4.1 Group II introns
15.3.5.4.2 Retrons
15.3.5.4.3 Diversity-generating retroelements
15.3.5.5 Interspersed Repeats
15.4 Eukaryotic Genome
15.4.1 Introduction
15.4.2 Packaging of DNA into Chromosome
15.5 Human Genome Project
15.5.1 Origin of the Project
15.5.2 Mapping of Human Genome
15.5.2.1 Mapping Strategies
15.5.2.1.1 Genetic Linkage Maps
15.5.2.2 Restriction Enzymes: Microscopic Scalpels
15.5.2.3 Physical Maps
15.5.2.4 Low-Resolution Physical Mapping
15.5.2.5 High-Resolution Physical Mapping
15.5.3 Sequence of Human Genome
15.5.3.1 Sources of DNA and Sequencing Methods
15.5.3.2 Genome Assembly Strategy and Characterization
15.5.4 Features of Human Genome
15.5.4.1 Noncoding DNA vs. Coding DNA
15.5.4.2 Coding Sequences (Protein-Coding Genes)
15.5.4.3 Noncoding DNA (ncDNA)
15.5.4.3.1 Pseudogenes
15.5.4.3.2 Untranslated Regions and Introns of mRNA
15.5.4.3.3 Regulatory DNA Sequences
15.5.4.3.4 Repetitive DNA Sequences
15.5.4.3.5 Transposons (Mobile Genetic Elements) and Their Remnants
15.5.5 Human HapMap Genome
15.5.6 Human Genome Vs. Chimpanzee Genome
15.6 Features of the Chloroplast Genome
15.6.1 Structure and Organization of the cpDNA
15.7 Features of Mitochondrial Genome
15.8 Comparative Genomics
Box 15.1: A HapMap Harvest of Insights into the Genetics of Common Disease-Teri A. Manolio et al.
15.8.1 Building a HapMap for the Human Genome
15.9 Summary
References
16: Application of Molecular Genetics
16.1 Biotechnology to Study Human Gene
16.1.1 Huntington´s Disease
16.1.2 Cystic Fibrosis
16.1.3 Sickle Cell Anemia
16.2 Biotechnology to Study Plants
16.2.1 Transgenic Crops
16.2.2 Herbicide Resistance
16.2.3 Insect Resistance
16.2.4 Production of Biofuels
16.3 Biotechnology to Study Pharma Product
16.3.1 Recombinant Insulin
16.3.2 Recombinant Growth Hormone
16.3.3 Recombinant Vaccine
16.3.4 Recombinant Protein
16.4 Biotechnology to Study Animals
16.4.1 Transgenic Animals
16.4.2 Improved Reproductive Rate
16.4.3 Improved Health
16.4.3.1 Vaccines
16.4.3.2 Diagnosis
16.4.4 Feed Additives
16.4.4.1 Antibiotics
16.4.4.2 Enzymes
16.4.4.3 Probiotics
16.4.4.4 Beta-agonists
16.5 Genetically Modified Organisms (GMOs)
16.5.1 Glowing Fish
16.5.2 GM Salmon
16.5.3 GM Mosquito
16.5.4 Eco-friendly Pig
16.5.5 Bird Flu-Resistant Chicken
16.5.6 Human Gene Therapy
16.5.7 Complications and Issues in Gene Therapy
16.6 Molecular Markers
16.6.1 Types of Nuclear Molecular Marker
16.6.1.1 Restriction Fragment Length Polymorphism (RFLP)
16.6.1.2 Random Amplification of Polymorphic DNA (RAPD)
16.6.1.3 Amplified Fragment Length Polymorphism (AFLP)
16.6.1.4 Sequence-Tagged Microsatellite
16.7 DNA Fingerprinting
16.8 Fluorescent in Situ Hybridization (FISH)
Box 16.1: Production of Recombinant Human Proinsulin in the Milk of Transgenic Mice (Qian X et al.)
16.9 Summary
Further Reading
17: Genetic Analysis of Development
17.1 Model Organism for Genetic Study
17.1.1 Yeast (Saccharomyces cerevisiae) (Fig. 17.1)
17.1.1.1 Saccharomyces cerevisiae
17.1.1.2 Saccharomyces cerevisiae: Structure and Components (Fig. 17.2)
17.1.1.3 Life Cycle and Reproduction (Fig. 17.3)
17.1.1.4 S. cerevisiae as an Effective Model Organism
17.1.1.5 Uses and Threats
17.1.2 Fruit Fly (Drosophila melanogaster) (Fig. 17.4)
17.1.2.1 Drosophila melanogaster: Structure and Components (Fig. 17.5)
17.1.2.2 Life Cycle and Reproduction (Fig. 17.6)
17.1.2.3 Drosophila melanogaster: An Efficient Model Organism
17.1.2.4 Threats
17.1.3 Nematode Worm (Caenorhabditis elegans) (Fig. 17.7)
17.1.3.1 Introduction
17.1.3.2 Caenorhabditis elegans: Structure and Components (Fig. 17.8)
17.1.3.3 Life Cycle and Reproduction (Fig. 17.9)
17.1.3.4 Caenorhabditis elegans: An Efficient Model Organism
17.1.3.5 Threats
17.1.4 Western Clawed Frog (Xenopus tropicalis) (Fig. 17.11)
17.1.4.1 Xenopus tropicalis: Structure and Components (Fig. 17.12)
17.1.4.2 Life Cycle and Reproduction (Fig. 17.13)
17.1.5 Xenopus tropicalis: An Efficient Model Organism
17.1.5.1 Threats
17.1.6 Mouse (Mus musculus) (Fig. 17.14)
17.1.6.1 Mus musculus: Structure and Components (Fig. 17.15)
17.1.6.2 Life Cycle and Reproduction (Fig. 17.16)
17.1.6.3 Mus musculus: As a Model Organism
17.1.6.4 Threats
17.1.7 Zebrafish (Danio rerio) (Fig. 17.17)
17.1.7.1 Danio rerio: Structure and Components (Fig. 17.18)
17.1.7.2 Life Cycle and Reproduction (Fig. 17.19)
17.1.7.3 Danio rerio: As a Model Organism
17.1.7.4 Threats
17.2 Mechanism of Gene Control in Development
17.2.1 Maternal Effect
17.2.2 Zygotic Gene Activity
17.2.2.1 Body Segmentation (Fig. 17.20)
17.2.2.2 Organ Formation (Fig. 17.21)
17.2.3 Analysis of Development in Vertebrates
17.2.3.1 Vertebrate Homologues
17.2.3.2 Mouse: Insertion Mutation
17.2.3.3 Mouse: Gene Knockout Mutation
17.2.3.4 Zebrafish: Gene Knockdown Mutation
17.2.3.5 Mammalian Stem Cell (Fig. 17.22)
17.2.3.5.1 Application of Stem Cells
17.2.3.5.2 Negative Concerns Regarding Stem Cell Therapy
17.2.4 Analysis of Developmental Result
17.2.4.1 Sex Determination in Drosophila
17.2.4.2 Dosage Compensation in Drosophila
17.2.4.3 Sex Determination in Mammals
17.2.4.4 Dosage Compensation in Mammals
17.2.4.5 Developmental Stages of Drosophila (Fig. 17.24)
17.2.4.6 Microarray Study of Drosophila Development
Box 17.1: Scientific Concept: Function of Drosophila ovo + in Germline Sex Determination Depends on X-Chromosome Number (Brian...
17.3 Summary
References
18: Molecular Genetics of Cancer
18.1 Cancer: Overview (Fig. 18.1)
18.2 Cancer Types
18.2.1 Gonadal Tumors
18.2.2 Classification of Cancer
18.2.3 Carcinoma
18.2.4 Immunotherapy
18.2.5 Sarcoma
18.2.6 Therapeutic Implications
18.2.7 Leukemia
18.2.8 Lymphoma
18.2.9 Therapeutic Targets
18.2.10 Lungs
18.2.11 Therapeutics
18.2.12 Female Breasts
18.2.13 Therapeutic Strategies
18.2.13.1 Chemotherapy
18.2.13.2 Hormone Therapy
18.2.13.3 Therapy Based on Antibody
18.2.13.4 Colon and Rectum
18.3 Cancer and Apoptosis
18.3.1 Morphological Changes in Apoptosis
18.3.2 Biochemical Changes in Apoptosis
18.3.3 Mechanism of Apoptosis
18.3.4 Apoptosis During Cancer
18.4 Telomere Shortening, Telomerase, and Cancer
18.4.1 TERT Expression: Epigenetic Regulation
18.4.2 Regulation of Gene Expression by Telomeres
18.4.3 TERT Promoter Mutations in Cancer
18.4.4 Telomere Shortening in Cancer
18.4.5 Telomerase Therapeutics
18.5 Carcinogens
18.6 Oncogenes
18.7 Viral Oncogenes
18.7.1 Human DNA Tumor Viruses
18.7.1.1 Human Papillomavirus (HPVs)
18.7.1.2 Epstein-Barr Virus (EBV)
18.7.1.3 Kaposi Sarcoma-Associated Herpesvirus (KSHV)
18.7.1.4 Human Polyomaviruses
18.7.1.5 Human Adenoviruses
18.7.1.6 Hepatitis B Virus (HBV)
18.7.2 Human RNA Tumor Viruses
18.7.2.1 HTLV-1
18.7.2.2 Xenotropic Murine Leukemia Virus-Related Virus (XMRV)
18.7.2.3 Hepatitis C Virus (HCV)
18.7.2.4 Rous Sarcoma Virus (RSV)
18.7.2.5 Avian Myelocytomatosis Virus MC29
18.7.2.6 Harvey Sarcoma Virus and Kirsten Sarcoma Virus
18.7.2.7 Abelson Murine Leukemia Virus
18.7.2.8 Avian Erythroblastosis Virus
18.7.2.9 Mode of Action of Viral Oncogenes
18.8 Proto-oncogenes
18.9 Mutant-oncogenes
18.9.1 Phosphatidylinositol 3-Kinase (PI3K)
18.9.2 Protein Kinase B (PKB)
18.9.2.1 B-RAF
18.9.2.2 RET
18.10 Tumor Suppressor Gene
18.10.1 PTEN
18.10.2 NF1
18.10.3 BRCA1 and BRCA2
18.10.3.1 APC
18.11 Two-Hit Hypothesis
18.12 RB1 Tumor Suppressor Gene
18.12.1 Clinical Characteristics and Diagnosis of Retinoblastoma
18.12.2 Structure and Function of RB1 Gene
18.12.3 Treatment Therapy
18.12.3.1 External Beam Radiation
18.12.3.2 Brachytherapy
18.12.3.3 Thermotherapy
18.12.3.4 Laser Photocoagulation
18.12.3.5 Cryotherapy
18.12.3.6 Chemothermotherapy
18.12.3.7 Chemotherapy
18.12.3.8 Enucleation
18.12.3.9 Targeted Approach with Small Molecules
18.13 p53 Tumor Suppressor Gene
18.13.1 The Physiological Functions of p53
18.13.2 Cell Cycle Regulation
18.13.3 Induction of Apoptosis
18.13.4 p53 Level and Activity Regulation
18.13.5 p53 Mutation
18.14 Cell Cycle and Cancer
18.14.1 Cell Cycle and Signal Transduction
18.14.2 Cell Cycle Checkpoints
18.14.2.1 The G1 and G1/S Checkpoint Responses
18.14.2.2 S Phase Checkpoint
18.14.2.3 The G2 Checkpoint
18.14.3 Cyclin D1 and Cyclin E Proto-oncogenes
Box 18.1: Scientific Concept: Cell Cycle Checkpoint Pathway Alterations in Breast Cancer (Gargi Dan Basu et al.)
18.15 Summary
References
Part IV: Population Genetics
19: Developmental Genetics
19.1 Genetic Approach of Development
19.1.1 Significance of Model Organism
19.1.2 Analysis of Developmental Mechanism
19.1.3 Developmental Genetics: Overview
19.2 Genetic Control of Eye Development
19.3 Drosophila: Embryonic Development
19.3.1 Overview
19.3.2 Anterior-Posterior Body Axis
19.3.3 Embryogenesis
19.4 Drosophila: Zygotic Gene
19.4.1 Gap Genes
19.4.2 Pair-Rule Genes
19.4.3 Segment Polarity Genes
19.5 Drosophila: Homeotic Gene
19.5.1 Hox Gene in Drosophila
19.5.2 Genetic Disorder in Humans
19.5.3 Control of Hox Gene Expression
19.6 Arabidopsis thaliana: Homeotic Gene
19.7 Caenorhabditis elegans: Development
19.8 Caenorhabditis elegans: Vulva Formation
19.9 Cell Signaling Network in Development
19.9.1 Wnt Pathway
19.9.2 Hedgehog Pathway
19.9.3 TGF-β Pathway
19.9.4 Receptor Tyrosine Kinase Pathway
19.9.5 Notch Pathway
Box 19.1: Scientific Concept: Variation and Constraint in Hox Gene Evolution (Heffer et al. 2013)
19.10 Summary
References
20: Quantitative Genetics
20.1 Introduction to Quantitative Genetics
20.1.1 Types of Quantitative Traits
20.1.2 Multiple Gene Hypothesis (or the Polygene Hypothesis)
20.1.3 Variation in a Quantitative Trait and the Number of Genetic Loci Involved
20.1.4 Examples of Polygenic Inheritance
20.1.5 Polygenic Traits and Oligogenic Traits
20.2 Statistical Analysis of Quantitative Traits
20.2.1 Frequency Distributions, Samples and Population
20.2.2 Mean, Median, Mode: Measures of Central Tendency
20.2.3 Variance and Standard Deviation: Measures of Dispersion
20.2.4 Correlation and Regression: Measures of Relation
20.2.5 ANOVA: Measure of Comparison
20.3 Components of Phenotypic Variance
20.3.1 Genetic Contribution to Phenotypic Variance
20.3.2 Environmental Contribution to Phenotypic Variance
20.3.2.1 External Environment
20.3.2.2 Internal Environment
20.3.2.3 General and Special Environmental Variance
20.3.3 Other Factors Contributing to Phenotypic Variance
20.4 Heritability
20.4.1 Types of Heritability
20.4.2 Factors Affecting Heritability
20.4.3 Measures of Heritability
20.5 Artificial Selection
20.6 Phenotypic and Genotypic Correlations
20.7 QTL Mapping
Box 20.1: Scientific Concept: Genetic Architecture of Natural Variation in Drosophila melanogaster Aggressive Behaviour - John...
20.8 Summary
References
Further Reading
21: Population Genetics
21.1 Identification of Genetic Variation
21.1.1 Single Nucleotide Polymorphism (SNP)
21.1.2 Microsatellite
21.1.3 Haplotype
21.1.4 The International HapMap Project
21.2 The Gene Pool Concept
21.3 The Hardy-Weinberg Equilibrium
21.3.1 Assumption of the Law
21.3.2 Prediction of the Law
21.3.3 Derivation of the Law
21.3.4 Extension of the Law with More than Two Alleles
21.3.5 Extension of the Law to X-Linked Alleles
21.3.6 Test for Hardy Weinberg Proportion
21.4 Mating System
21.4.1 According to Index Value
21.4.1.1 Positive Assortative Mating
21.4.1.2 Negative Assortative Mating
21.4.2 According to Relationship
21.4.2.1 Line Breeding
21.4.2.2 Deliberate Inbreeding
21.4.2.3 Inbreeding Avoidance
21.4.3 Crossbreeding
21.4.3.1 Single Cross
21.4.3.2 Terminal Sire System
21.4.3.3 Composite Breed
21.5 Measurement of Genetic Variation
21.5.1 At Protein Level
21.5.2 At DNA Level
21.6 Modulation of Genetic Variation
21.6.1 Mutation
21.6.2 Genetic Drift
21.6.3 Balance Between Mutation and Drift
21.6.4 Migration
21.6.5 Natural Selection
21.6.6 Balance Between Mutation and Selection
21.7 Conservation Genetics
21.7.1 Ex Situ Conservation: Captive Breeding
21.7.2 Ex Situ Conservation: Gene Bank
21.7.3 In Situ Conservation
Box 21.1: Scientific Concept: Analysis of Genetic Variation and Potential Applications in Genome-Scale Metabolic Modelling - J...
21.8 Chapter Summary
References
22: Evolutionary Genetics
22.1 Concept of Evolution
22.1.1 Theories of Evolution: Lamarckism
22.1.2 Theories of Evolution: Darwinism and Neo-Darwinism
22.2 Genetic Variation in Population
22.2.1 Continuous Vs. Discontinuous Variations (Table 22.1)
22.2.2 Environmental Variations
22.2.3 Mutational Variations
22.2.4 Recombination
22.3 The Neutral Theory of Molecular Evolution
22.3.1 Neutral Theory
22.3.2 Rate of Neutral Substitution and Molecular Clock
22.4 Natural Selection
22.4.1 Directional, Stabilizing and Disruptive Selection
22.4.1.1 Directional/Progressive Selection (Under Changing Environmental Conditions)
22.4.1.2 Stabilizing/Normalizing/Centripetal Selection (Under Constant Environmental Conditions)
22.4.1.3 Disruptive/Diversifying/Centrifugal Selection (Under Heterogeneous Environmental Conditions)
22.4.2 Kin and Group Selection
22.4.2.1 Kin Selection
22.4.2.2 Group Selection
22.4.3 Sexual Selection
22.4.4 Concept of Fitness, Selection Coefficient, Genetic Load and Genetic Death
22.4.4.1 Fitness
22.4.4.2 Selection Coefficient
22.4.4.3 Genetic Load and Genetic Death
22.5 Population Genetics
22.5.1 Hardy-Weinberg Model
22.5.1.1 Application of Hardy-Weinberg Law on Human Population
22.5.2 Genetic Drift
22.5.2.1 Founder´s Effect
22.5.2.2 Bottleneck Effect
22.5.3 Role of Mutation and Migration in Changing Allele Frequency
22.5.3.1 Mutation
22.5.3.2 Migration
22.5.4 Impact of Positive Selection
22.6 Speciation
22.6.1 Definition of Species
22.6.1.1 Typological Species Concept
22.6.1.2 Biological Species Concept
22.6.1.3 Recognition Species Concept
22.6.1.4 Morphological Species Concept
22.6.1.5 Ecological Species Concept
22.6.2 Modes of Speciation
22.6.3 Isolating Mechanisms
22.6.4 Genetics of Speciation and Reproductive Isolation
22.7 Evolution of Man
22.8 Concept of Molecular Phylogeny
22.8.1 Phylogenetic Tree
22.8.1.1 Objectives of Molecular Phylogeny
22.8.2 Types of Tree Representation
22.8.2.1 Clade
22.8.3 Procedure for Tree Construction
Box 22.1: Scientific Concept
22.9 Summary
References