Lehninger: Principles of Biochemistry


1. The Foundations of Biochemistry
1.1. Cellular Foundations
1.2. Chemical Foundations
1.3. Physical Foundations
1.4. Genetic Foundations
1.5. Evolutionary Foundations

I. STRUCTURE AND CATALYSIS

2. Water
2.1. Weak Interactions in Aqueous Solution
2.2. Ionization of Water, Weak Acids, and Weak Bases
2.3. Buffering against pH Changes in Biological systems
2.4. Water as a Reactant
2.5. The Fitness of the Aqueous Environment for Living Organisms

3. Amino Acids, Peptides and Proteins
3.1. Amino Acids
3.2. Peptides and Proteins
3.3. Working with Proteins
3.4. The Structure of Proteins: Primary Structure

4. The Three-Dimensional Structure of Proteins
4.1. Overview of Protein Structure
4.2. Protein Secondary Structure
4.3. Protein Tertiary and Quaternary Structures
4.4. Protein Denaturation and Folding

5. Protein Function
5.1. Reversible Binding of a Protein to a Ligand: Oxygen-Binding Proteins
5.2. Complementary Interactions between Proteins and Ligands: The Immune System and Immunoglobulins
5.3. Protein Interactions Modulated by Chemical Energy: Actin, Myosin, and Molecular Motors

6. Enzymes
6.1. An Introduction to Enzymes
6.2. How Enzymes Work
6.3. Enzyme Kinetics as an Approach to Understanding Mechanism
6.4. Examples of Enzymatic Reactions
6.5. Regulatory Enzymes

7. Garbohydrates and Glycobiology
7.1. Monosaccharides and Disaccharides
7.2. Polysaccharides
7.3. Glycoconjugates: Proteoglycans, Glycoproteins and Glycolipids
7.4. Carbohydrates as Informational Molecules: The Sugar Code
7.5. Working with Carbohydrates

8. Nucleotides and Nucleic Acids
8.1. Some Basics
8.2. Nucleic Acid Structure
8.3. Nucleic Acid Chemistry
8.4. Other Functions of Nucleotides

9. DNA-Based Information Technologies
9.1. DNA Clonning: The Basics
9.2. From Genes to Genomes
9.3. From Genomes to Proteomes
9.4. Genome Alterations and New Products of Biotechnology

10. Lipids
10.1. Storage Lipids
10.2. Structural Lipids in Membranes
10.3. Lipids as Signals, Cofactors, and Pigments
10.4. Working with Lipids

11. Biological Membranes and Transport
11.1. The Composition and Architecture of Membranes
11.2. Membrane Dynamics
11.3. Solute Transport across Membranes

12. Biosignaling
12.1. General Features of Signal Transduction
12.2. G Protein-Coupled Receptors and Second Messengers
12.3. Receptor Tyrosine Kinases
12.4. Receptor Guanylyl Cyclases, cGMP, and Protein Kinase G
12.5. Multivalent Adaptor Proteins and Membrane Raffts
12.6. Gated Ion Channels
12.7. Integrins: Bidirectional Cell Adhesion Receptors
12.8. Regulation of Transcription by Steroid Hormones
12.9. Signaling in Microorganisms and Plants
12.10. Sensory Transduction in Vision, Olfaction, and Gustation
12.11. Regulation of the Cell Cycle by Protein Kinases
12.12. Oncogenes, Tumor Supressor Genes, and Programmed Cell Death

II BIOENERGETICS AND METABOLISM

13. Bioenergetics and Biochemical Reaction Types
13.1. Bioenergetics and Thermodynamics
13.2. Chemical Logic and Common Biochemical Reactions
13.3. Phosphoryl Group Transfer and ATP
13.4. Biological Oxidation-Reduction Reactions

14. Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway
14.1. Glycolysis
14.2. Feeder Pathways for Glycolysis
14.3. Fates of Pyruvate under Anaerobic Conditions: Fermentation
14.4. Glugoneogenesis
14.5. Pentose Phosphate Pathway of Glucose Oxidation

15. Principles of Metabolic Regulation
15.1. Regulation of Metabolic Pathways
15.2. Analysis of Metabolic Control
15.3. Coordinated Regulation of Glycolysis and Gluconeogenesis
15.4. The Metabolism of Glycogen in Animals
15.5. Coordinated Regulation of Glycogen Synthesis and Breakdown

16. The Citric Acid Cycle
16.1. Production of Acetyl-CoA (Activated Acetate)
16.2. Reactions of the Citric Acid Cycle
16.3. Regulation of the Citric Acid Cycle
16.4. The Glyoxylate Cycle

17. Fatty Acid Catabolism
17.1. Digestion, Mobilization, and Transport of Fats
17.2. Oxidation of Fatty Acids
17.3. Ketone Bodies

18. Amino Acid Oxidation and the Production of Urea
18.1. Metabolic Fates of Amino Groups
18.2. Nitrogen Excretion and the Urea Cycle
18.3. Pathways of Amino Acid Degradation

19. Oxidative Phosphorylation and Photophosphorylation

OXIDATIVE PHOSPHORYLATION
19.1. Electron-Transfer Reactions in Mitochondria
19.2. ATP Synthesis
19.3. Regulation of Oxidative Phosphorylation
19.4. Mitochondria in Thermogenesis, Steroid Synthesis, and Apoptosis
19.5. Mitochondrial Genes: Their Origin and the Effects of Mutations

PHOTOSYNTHESIS: HARVESTING LIGHT ENERGY
19.6. General Features of Photophosphorylation
19.7. Light Absorption
19.8. The Central Photochemical Event: Light-Driven Electron Flow
19.9. ATP Synthesis by Photophosphorylation
19.10. The Evolution of Oxygenic Photosynthesis

20. Carbohydrate Biosynthesis in Plants and Bacteria
20.1. Photosynthetic Carbohydrate Synthesis
20.2. Photorespiration and the C4 and CAM Pathways
20.3. Biosynthesis of Starch and Sucrose
20.4. Synthesis of Cell Wall Polysaccharides: Plant Cellulose and Bacterial Peptidoglycan
20.5. Integration of Carbohydrate Metabolism in the Plant Cell

21. Lipid Biosynthesis
21.1. Biosynthesis of Fatty Acids and Eicosanoids
21.2. Biosynthesis of Triacylglycerols
21.3. Biosynthesis of Membrane Phospholipids
21.4. Biosynthesis of Cholesterol, Steroids, and Isoprenoids

22. Biosynthesis of Amino Acids, Nucleotides, and Related Molecules
22.1. Overview of Nitrogen Metabolism
22.2. Biosynthesis of Amino Acids
22.3. Molecules Derived from Amino Acids
22.4. Biosynthesis and Degradation of Nucleotides

23. Hormonal Regulation and Integration of Mammalian Metabolism
23.1. Hormones: Diverse Structures for Diverse Functions
23.2. Tissue-Specific Metabolism: The Division of Labour
23.3. Hormonal Regulation of Fuel Metabolism
23.4. Obesity and the Regulation of Body Mass
23.5. Obesity, the Metabolic Syndrome, and Type 2 Diabetes

III INFORMATIVE PATHWAYS

24. Genes and Chromosomes
24.1. Chromosomal Elements
24.2. DNA Supercoiling
24.3. The Structure of Chromosomes

25. DNA Metabolism
25.1. DNA Replication
25.2. DNA Repair
25.3. DNA Recombination

26. RNA Metabolism
26.1. DNA-Dependent Synthesis of RNA
26.2. RNA Processing
26.3. RNA-Dependent Synthesis of RNA and DNA

27. Protein Metabolism
27.1. The Genetic Code
27.2. Protein Synthesis
27.3. Protein Targeting and Degradation

28. Regulation of Gene Expression
28.1. Principles of Gene Regulation
28.2. Regulation of Gene Expression in Bacteria
28.3. Regulation of Gene Expression in Eukaryotes

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