1 The Chemical Foundations of Biochemistry
Chemistry in Context
1.1 General Chemical Principles
1.2 Fundamental Concepts of Organic Chemistry
1.3 The Chemistry of Water
2 Nucleic Acids
Nucleic Acids in Context
Nucleic acids are the Genetic Materials
2.1 Nucleic Acids Have Distinct Structures
2.2 Nucleic Acids Have Many Cellular Functions
2.3 The Manipulation of Nucleic Acids Has Transformed Biochemistry
3 Proteins I: An Introduction to Protein Structure, Function, and its Purification
Proteins in Context
3.1 Amino Acid Chemistry
3.2 Proteins Are Polymers of Amino Acids
3.3 Proteins Are Molecules of Defined Shape and Structure
3.4 Examples of Protein Structures and Functions
3.5 Protein Purification Basics
3.6 Size-Exclusion Chromatography
3.7 Affinity Chromatography
4 Proteins II: Enzymes
Enzymes in Context
4.1 Introduction to Enzymes
4.2 Enzymes Increase Reaction Rate
4.3 The Mechanism of an Enzyme Can Be Deduced from Structural, Kinetic, and Spectral Data
4.4 Examples of Enzyme Regulation
4.5 Allosterism and Cooperativity
4.6 Hemoglobin
4.7 Receptor–Ligand Interactions
5 Membranes and an Introduction to Signal Transduction
Biochemistry in Context
5.1 Membrane Structure and Function
5.2 Signal Transduction
6 Carbohydrates I: Mono- and Disaccharides, Glycolysis, Gluconeogenesis, and the Fates of Pyruvate
Carbohydrates in Context
6.1 Properties, Nomenclature, and Biological Functions of Monosaccharides
6.2 Properties, Nomenclature, and Biological Functions of Complex Carbohydrates
6.3 Glycolysis and an Introduction to Metabolic Pathways
6.4 Gluconeogenesis
6.5 The Fates of Pyruvate
7 The Common Catabolic Pathway: Citric Acid Cycle, the Electron Transport Chain, and ATP Biosynthesis
Electron Transport in Context
7.1 The Citric Acid Cycle
7.2 The Electron Transport Chain
7.3 ATP Biosynthesis
8 Carbohydrates II: Glycogen Metabolism, the Pentose Phosphate Pathway, Glycoconjugates, and Extracellular Matrices
Polysaccharides in Context
8.1 Glycogen Metabolism
8.2 The Pentose Phosphate Pathway
8.3 Carbohydrates in Glycoconjugates
8.4 Extracellular Matrices and Biofilms
9 Lipids I: Fatty Acids, Steroids, and Eicosanoids; Beta-Oxidation and Fatty Acid Biosynthesis
Lipids in Context
9.1 Properties, Nomenclature, and Biological Functions of Lipid Molecules
9.2 Fatty Acid Biosynthesis
9.3 Fatty Acid Catabolism
9.4 Ketone Body Metabolism
9.5 Steroid Metabolism
9.6 Eicosanoid and Endocannabinoid Metabolism
10 Lipids II: Metabolism and Transport of Complex Lipids
Complex Lipids in Context
10.1 Phospholipid Metabolism
10.2 Digestion of Triacylglycerols
10.3 Transport of Lipids in the Circulation
10.4 Entry of Lipids into the Cell
10.5 Neutral Lipid Biosynthesis
10.6 Lipid Storage Droplets, Fat Storage, and Mobilization
10.7 Lipid Rafts as a Biochemical Entity
11 Amino Acid and Amine Metabolism
Amine Metabolism in Context
11.1 Digestion of Proteins
11.2 Amino Acid Deamination and Transamination
11.3 The Urea Cycle
11.4 Metabolism of Amino Acid Carbon Skeleton
11.5 The Detoxification of Other Amines and Xenobiotics
11.6 The Biochemistry of Renal Function
12 Regulation and Integration of Metabolism
Metabolism in Context
12.1 A Review of the Pathways and Crossroads of Metabolism
12.2 Organ Specialization and Metabolic States
12.3 Communication between Organs
12.4 Metabolic Disease
13 Nucleotide and Deoxynucleotide Metabolism
Nucleotides and Deoxynucleotides in Context
13.1 Purine Biosynthesis
13.2 Pyrimidine Biosynthesis
13.3 Deoxyribonucleotide Biosynthesis
13.4 Catabolism of Nucleotides
14 DNA Replication, Damage, and Repair
DNA in Context
14.1 Challenges of DNA Replication
14.2 DNA Replication in Prokaryotes
14.3 DNA Replication in Eukaryotes
14.4 DNA Damage and Repair
14.5 Homologous Recombination
15 RNA Synthesis and Processing
RNA Synthesis in Context
15.1 Transcription: RNA Synthesis
15.2 Processing of Nascent Eukaryotic RNA Messages
15.3 RNA Export from the Nucleus
16 Protein Biosynthesis
Protein Synthesis in Context
16.1 The Genetic Code
16.2 Machinery Involved in in Protein Biosynthesis
16.3 Mechanism of Protein Biosynthesis
17 Control and Regulation of Gene Expression
Gene Regulation in Context
17.1 DNA--Protein Interactions
17.2 Regulation of Gene Expression in Prokaryotes
17.3 Regulation of Gene Expression in Eukaryotes
18 Determination of Macromolecular Structure
Macromolecular Structure in Context
18.1 An Introduction to Structure Determination
18.2 Electron Microscopy—Types and Advantages
18.3 X-Ray Diffraction and Neutron Scattering
18.4 Nuclear Magnetic Resonance
19 Protein Production, Engineering and Folding
Protein Production, Engineering and Folding in Context
19.1 Protein Production
19.2 Protein Engineering
19.3 Protein Folding
20 Bioinformatics and Omics
Bioinformatics in Context
20.1 Introduction to Bioinformatics
20.2 Generating Bioinformatic Data
20.3 Analyzing Bioinformatic Data
21 Signal Transduction
Cell Signaling in Context
21.1 A Review of Signal Transduction
21.2 An Overview of Regulation of Signal Transduction
21.3 Six New Signal Transduction Pathways
22 Protein Trafficking
Protein Trafficking in Context
22.1 Molecular Aspects of Protein Trafficking
22.2 Molecular Motor Proteins
22.3 Vesicular Fusion
23 Photosynthesis and Nitrogen Fixation
Photosynthesis and Nitrogen Fixation in Context
23.1 Photosynthesis
23.2 Nitrogen Fixation
Techniques
Solutions
Glossary
Index