The Evolution of Molecular Biology

CHAPTER 1 BEGINNINGS Some ancient intuitions Spontaneous generation Vitalism The demise of vitalism The rise of modern biology The microscope opens a new world

CHAPTER 2 THE ORIGINS OF BIOCHEMISTRY Recognition of proteins Some proteins are catalysts: Enzymes What enzymes do, and why it is so important How do enzymes work? Proteins fulfill many roles What are proteins made of?

CHAPTER 3 THE CHEMICAL STRUCTURE OF PROTEINS The peptide hypothesis Colloid or macromolecule? Some unexpected results Proteins as homogeneous polypeptides Fred Sanger and the sequence of insulin Boxes: Box.3.1 Separation MethodsA: SedimentationB: Chromatography C: ElectrophoresisBox 3.2 Immunological methods

CHAPTER 4 PROTEINS IN THREE DIMENSIONS Fibers Globules The first globular protein structures Boxes:Box 4.1 How to Determine Protein StructureA. The principle of diffractionB. Diffraction from fibersC. Diffraction from crystals

CHAPTER 5 THE ORIGINS OF GENETICS Classical genetics and the rules of trait inheritance Friar Gregor Mendel plants some peas Mendel formulates the two laws of inheritance Mendel’s laws have extensions and exceptions Mendel was long ignored Darwin, Mendelism, and mutations Genes are arranged linearly on chromosomes and can be mapped What do genes do, and what are they made of?

CHAPTER 6 NUCLEIC ACIDS Miescher's mysteries The chemical structures of nucleic acids “What is life?” DNA carries genetic information Mysterious numbers Boxes:Box 6.1 Gel electrophoresis

CHAPTER 7 THE GREAT SYNTHESIS Bacteria and viruses have genetics, too: the introduction of cloning Critical experiments show that the genetic material is DNA Revealing DNA structure; perspiration plus inspiration "It has not escaped our attention..." The most beautiful experiment DNA sequence and protein sequence; a tale of two languages Methods Box: Reading a helix and chasing replication

CHAPTER 8 HOW DNA IS REPLICATED What is the mode of replication? How does replication proceed? The lagging strand problem

CHAPTER 9 THE CENTRAL DOGMA Speaking in different languages Intuiting a dogma Who is the Messenger? The great decade: 1952-1962

CHAPTER 10 THE GENETIC CODE How might a code function? What kind of code? What were the code words? The code

CHAPTER 11 GENE TO PROTEIN: THE WHOLE PATH What was known in 1960? Breakthrough The rest of the story Regulation of transcription in bacteria Overview

CHAPTER 12 EUKARYOTES POSE NEW PROBLEMS What is a eukaryote? The origin of eukaryotes The three domains of life Interrupted messages and splicing Every cell type has special needs and functions Multiple levels of control Chromatin and nucleosomes Too much DNA? Junk DNA?

CHAPTER 13 DIFFERENTIATION AND DEVELOPMENT Two Ideas about development dominated thinking in ancient times The Introduction of scientific approaches to the field of development An opportunity missed? What do we know about development and differentiation at present? Embryonic stem cells (ESC) serve as a model for pluripotency The Molecular Basis of Differentiation and Development• The maternal-zygotic transition• Genes control development: the case for the fruit fly Nuclear transfer experiments and the principle of genetic equivalence Genome reprogramming towards earlier phases of development is possible

CHAPTER 14 RECOMBINANT DNA: THE NEXT REVOLUTION The power of DNA recombination  How to clone DNA Construction of recombinant DNA molecules needs restriction endonucleases and ligases The first recombinant DNA molecules Polymerase chain reaction and site-directed mutagenesis Manipulating the genetic content of eukaryotic organisms CRISPR, the gene-editing technology of today and tomorrow Boxes:Box 12.1: Cloning vectors. The expression of recombinant genes.

CHAPTER 15 UNDERSTANDING WHOLE GENOMES: CREATING NEW PARADIGMS The evolution of sequencing methodology Genomic libraries contain the entire genome of an organism as a collection of recombinant DNA molecules There are two classic approaches for sequencing large genomes Ultrafast sequencing allows deep analysis of genomes Whole genomes The human genome project ENCODE results raise question. Whence biology? So, what was learned from ENCODE? Transcription factors interact in a huge network Where is ENCODE leading? Attempts at a contemporary definition of a gene Boxes:Box 15.1 The classic definition of a gene is not consistent with recent observationsCHAPTER 16 WHOLE GENOMES AND EVOLUTION Evolutionary theory: from Darwin to the present day Classifying organisms: Phylogenetics Phylogenetics goes molecular The comparative genomics revolution Tracing human evolution

CHAPTER 17 PRACTICAL APPLICATIONS OF RECOMBINANT DNA TECHNOLOGIES Catching criminals and freeing the innocent Production of pharmaceutical compounds in recombinant bacteria or yeast Genetic engineering of plants Gene therapy A CRISPR revolution? Cloning of whole animals Jurassic park or de-extinction