Chapter 1 From Classical Genetics to Molecular Genetics 1.1 Introduction 1.2 Classical genetics and the rules of trait inheritance 1.2.1 Gregor Mendel developed the formal rules of genetics 1.2.2 Mendel's laws have extensions and exceptions 1.2.3 Genes are arranged linearly on chromosomes and can be mapped 1.2.4 The nature of genes and how they determine phenotypes was long a mystery 1.3 The great breakthrough to molecular genetics 1.3.1 Bacteria and bacteriophage exhibit genetic behavior and serve as model systems 1.3.2 Transformation and transduction allow transfer of genetic information 1.3.3 The Watson-Crick model of DNA structure provided the final key to molecular genetics Chapter 2 Structures and Functions of Proteins and Nucleic Acids 2.1 Introduction 2.2 Proteins 2.2.1 Amino acids and peptides 2.2.2 Levels of structure in the polypeptide chain 2.2.3 Protein folding 2.2.4 Protein destruction 2.3 Nucleic acids 2.3.1 Chemical structure of nucleotides 2.3.2 Physical structure of DNA 2.3.3 Physical structures of RNA 2.3.4 One-way flow of genetic information 2.3.5 Methods used to study nucleic acids Chapter 3 Recombinant DNA: Principles and Applications 3.1 Introduction of homologous recombination and cloning 3.1.1 The beginnings of recombinant DNA technology 3.1.2 Homologous recombination and cloning 3.2 Construction of recombinant DNA molecules 3.2.1 Major classes of restriction endonucleases 3.2.2 Recognition sequences for type II restriction endonucleases 3.2.3 DNA ligase joins linear pieces of DNA 3.2.4 Sources of DNA for cloning 3.3 Vectors for cloning 3.3.1 Genes coding for selectable markers are inserted into vectors during their construction 3.3.2 Plasmid DNA were the first cloning vector 3.3.3 Recombinant bacteriophages can serve as vectors 3.3.4 Cosmids and phagemids expand the repertoire of cloning vector 3.4 Expression of recombinant genes 3.4.1 Expression vectors allow regulated and efficient expression of cloned genes 3.4.2 Expression systems 3.5 Introducing recombinant DNA into host cells 3.5.1 Numerous host-specific techniques are used to introduce recombinant DNA molecules into living cells 3.5.2 Transient and stable transfection assays 3.6 Constructing DNA libraries 3.6.1 Type of different libraries 3.6.2 Library screening and probes 3.7 Sequencing of entire genomes 3.7.1 Genomic libraries contain the entire genome of an organism as a collection of recombinant DNA molecules 3.7.2 There are two approaches for sequencing large genomes 3.8 Practical application of recombinant DNA technologies 3.8.1 Gene therapy 3.8.2 Delivering a gene into sufficient cells within a specific tissue and ensuring its subsequent long-term expression is a challenge Chapter 4 Tools for Analyzing Gene Expression 4.1 Introduction 4.2 Gene isolation and detection 4.2.1 Agarose gel electrophoresis of DNA 4.2.2 Gradient centrifugation 4.2.3 Nucleic acid hybridization 4.2.4 Polymerase chain reaction 4.2.5 In vitro mutagenesis 4.2.6 DNA sequencing 4.3 Analysis at the level of gene transcription: RNA expression and localization 4.3.1 Reverse transcription PCR 4.3.2 Northern blotting 4.3.3 RNase protection assay (RPA) 4.3.4 In situ hybridization 4.3.5 DNA microarrays 4.4 Analysis of the transcription rates 4.4.1 S1 nuclease protection and primer extension 4.4.2 Rapid amplification of cDNA ends , 4.4.3 Reporter genes 4.4.4 DNA footprinting 4.4.5 Electrophoretic mobility shift assay 4.4.6 Chromatin immunoprecipitation 4.5 Analysis at the level of translation: protein expression and localization 4.5.1 Western blotting 4.5.2 Enzyme-linke
