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 Methods
A: Sedimentation
B: Chromatography 
C: Electrophoresis
Box 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 Structure
A. The principle of diffraction
B. Diffraction from fibers
C. 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 observations
CHAPTER 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