Biochemistry

Contents:

Preamble

Preface

Abbreviations

How to use this book

Chapter 1: Biochemistry in the modern world • What is biochemistry? • Chemistry is also important in biochemistry • Box 1.1 The origins of biochemistry • Box 1.2 Schrödinger  and biology • Biochemistry involves the study of very large biomolecules • Box 1.3 Atoms, isotopes and molecular masses • Biochemistry is also the study of metabolism • The storage and utilization of biological information is an important part of biochemistry • Biochemistry is an experimental science • Box 1.4 Omes are collections of biomolecules • Further reading

PART 1: Cells, organisms and biomolecules

Chapter 2: Cells and organisms • Cells the building blocks of life • Box 2.1 Units of measurement • There are two different types of cell structure • Box 2.2 Species names • Prokaryotes • Box 2.3 Bacteria communicate with one another in a biofilm • Box 2.4 The microbiome • Eukaryotes • What about viruses? • Box 2.5 Unusual types of infectious particles • Evolution and the unity of life • Life originated four billion years ago • Three and a half billion years of evolution • Box 2.6 Mass extinction events • Further reading • Self-assessment questions

Chapter 3: Proteins • Proteins are made of amino acids • Twenty different amino acids are used to make proteins • The biochemical features of amino acids • Box 3.1 Are there two versions of every amino acid? • Box 3.2 The ionization of water and the pH scale • Some amino acids are modified after protein synthesis • Box 3.3 Types of chemical bond • The primary and secondary levels of protein structure • Polypeptides are polymers of amino acids • Polypeptides can take up regular conformations • Box 3.4 The unusual characteristics of the peptide bond • Box 3.5 What is the difference between a left-handed and a right-handed helix? • Box 3.6 Predicting the secondary structure of polypeptide from its amino acid sequence • Fibrous and globular proteins • Fibrous proteins: keratin, collagen and silk • Globular proteins have tertiary and possibly quaternary structures • Box 3.7 Using collagen structure to identify extinct animals • Box 3.8 An example of a protein with a mixture of domains • Protein folding • Small proteins fold spontaneously into their correct tertiary structures • Protein folding pathways • Box 3.9 Studying protein folding • Protein folding is one of the fundamental principles of biology • Further reading • Self-assessment questions

Chapter 4: Nucleic acids • The structures of DNA and RNA • Polynucleotide structure • DNA and RNA secondary structures • Box 4.1 Base stacking • Box 4.2 The discovery of the double helix • Box 4.3 Sugar pucker • Box 4.4 Units of length for nucleic acid molecules • RNAs display a diverse range of chemical modifications • Packaging of DNA • Nucleosomes and chromatin fibers • Box 4.5 DNA packaging in bacteria • Further reading • Self-assessment questions

Chapter 5: Lipids and biological membranes • Lipid structures • Fatty acids and their derivatives • Box 5.1 Structural notation for fatty acids • Box 5.2 Essential fatty acids • Diverse lipids with diverse functions • Box 5.3 Polyterpenes • Box 5.4 Prostaglandins • Biological membranes • Membrane structure • Box 5.5 The carbohydrate component of a membrane • Membranes as selective barriers • Box 5.6 Voltage-gated ion channels and nerve impulses • Box 5.7 The biochemistry of cystic fibrosis • Further reading • Self-assessment questions

Chapter 6: Carbohydrates • Monosaccharides, disaccharides and oligosaccharides • Monosaccharides are the building blocks of carbohydrates • Box 6.1 Representations of monosaccharide structures • Box 6.2 The different types of isomers relevant to carbohydrate structure • Disaccharides are made by linking together pairs of monosaccharides • Box 6.3 Some humans have recently evolved the ability to digest milk • Oligosaccharides are short monosaccharide polymers • Polysaccharides • Starch, glycogen, cellulose and chitin are homopolysaccarides • Box 6.4 The reducing and non-reducing ends of a starch molecule • Heteropolysaccharides are found in the extracellular matrix and in bacterial cell walls • Further reading • Self-assessment questions