CUPRINS PRINCIPLES OF BIOCHEMISTRY
Chapter 1: The foundations of biochemistry 1
Cellular foundations 3
Chemical foundations 12
Physical foundations 21
Genetic foundations 28
Evolutionary foundations 31
Structure and catalysis
Chapter 2: Water 47
Weak interactions in aqueous systems 47
Ionizations of water, weak acids, and weak bases 60
Buffering against pH changes in biological systems 65
Water as a reactant 69
The fitness of aqueous environment for living organisms 70
Chapter 3: Amino acids, peptides and proteins 75
Amino acids 75
Peptides and proteins 85
Working with proteins 89
The covalent structure of proteins 96
Proteins sequences and evolution 106
Chapter 4: The three dimensional structure of proteins 116
Overview of protein structure 116
Protein secondary structure 120
Protein tertiary and quaternary structure 125
Protein denaturation and folding 147
Chapter 5: Protein functions 157
Reversible binding of a protein to a ligand: oxygen binding proteins 158
Complementary interactions between proteins and ligands: the immune sustem and immunoglobulins
174
Protein interaction modulated by chemical energy: actin, myosin, and molecular motors 184
Chapter 6: Enzymes 190
An introduction to enzymes 191
How enzymes work 193
Enzyme kinetics as an approach to understanding mechanisms 202
Examples of enzymatic reactions 213
Regulatory enzymes 225
Chapter 7: Carbohydrates and glycobiology 238
Monosaccharides and disaccharides 239
Polysaccharides 247
Glycoconjugates: proteoglycans, glycoproteins and glycolipids 255
Carbohydrates as informational molecules: the sugar code 261
Working with carbohydrates 267
Chapter 8: Nucleotides and nucleic acids 273
Some basics 273
Nucleic acid structure 279
Nucleic acid chemistry 291
Other functions of nucleotides 300
Chapter 9: DNA-based information tehnologies 306
DNA cloning: the basics 306
From genes to genoms 317
From genomes to proteomes 325
Genome alterations and other products of biotechnology 330
Chapter 10: Lipids 343
Storage lipids 343
Structural lipids in membranes 348
Lipids as signals, cofactors, and pigments 357
Working with lipids 363
Chapter 11: Biological membranes and transport 369
The composition and architecture of membranes 370
Membrane dynamics 380
Solute transport across membranes 389
Chapter 12: Biosignaling 421
Molecular mechanisms of signal transduction 422
Gated ion chanels 425
Receptor enzymes 429
G-protein-coupled receptors and secondary messengers 435
Multivalent scaffold proteins and membrane rafts 443
Signaling in microorganisms and plants 452
Sensory signaling in vision, olfaction and gustation 456
Regulation of transcription by steroid hormones 465
Regulation of the cell cycle by protein kinases 466
Oncogenes, tumor suppressor genes, and programed cell death 471
Bioenergetics and metabolism part II
Chapter 13: Principles of bioenergetics 480
Bioenergetics and thermodynamics 490
Phosphoryl group transfers and ATP 496
Biological oxidation-reduction reactions 507
Chapter 14: Glycolisis, gluconeogenesis and the pentose phosphate pathway 521
Glycolisis 521
Feeder pathways to glycolisis 534
Fates of pyruvate under anaerobic conditions: fermentation 538
Gluconeogenesis 543
Pentose phosphate pathway of glucose oxidation 549
Chapter 15: Principles of metabolic regulation, illustrated with the metabolism of glucose and
glycogen 560
The metabolism of glycogen in animals 562
Regulation of metabolic pathways 571
Coordinated regulation of glycolisis and gluconeogenesis 575
Coordonated regulation of glycogen synthesis and breakdown 583
Analysis of metabolic control 591
Chapter 16: The citric acid cycle 601
Production of acetyl-CoA (activated acetate) 602
Reactions of the citric acid cycle 606
Regulation of the cittic acid cycle 621
The glyoxilate cycle 623
Chapter 17: Fatty acid catabolism 631
Digestion, mobilisation, and transpprt of fats 632
Oxidation of fatty acids 637
Ketone bodies 650
Chapter 18: Amino acid oxidation and the production of ureea 656
Metabolic fates of amino groups 657
Nitrogen excretion and the ureea cycle 665
Pathways of amino acid degradation 671
Chapter 19: Oxidative phosphorylation and photophosphorylation 690
Oxidative phosphorylation
Electron-transfer reactions in mitochondria 691
ATP synthesis 704
Regulation of oxidative phosphorylation 716
Mitochondrial genes: their origin and the effects of mutations 719
The role of mitochondria in apoptosis and oxidative stress 721
Photosynthesis: harvesting light energy
General features of photophosphorylation 723
Light absorption 725
The central photochemical event: light-driven electron flow 730
ATP synthesis by photophosphorylation 740
Chapter 20: Carbohydrate biosynthesis in plants and bacteria 751
Photosynthetic carbohydrate synthesis 751
Photorespiration and the C4 and CAM pathways 766
Biosynthesis of starch and sucrose 771
Synthesis of cell wall polysaccharides: cellulose and bacterial peptidoglycan 775
Integration of the carbohydrate metabolism in the plant cell 780
Chapter 21: Lipid biosynthesis 787
Biosynthesis of fatty acids and eicosanoids 787
Biosynthesis of triacylglycerols 804
Biosynthesis of membrane phospholipids 808
Biosynthesis of cholesterol, steroids, and isoprenoids 816
Chapter 22: Biosynthesis of amino acids, nucleotides and related molecules 833
Overview of nitrogen metabolism 834
Biosynthesis of amino acids 841
Molecules derived from amino acids 854
Biosynthesis and degradation of nucleotides 862
Chapter 23: Integration and hormonal regulation of mammalian metabolism 881
Hormones: diverse structures for diverse functions 881
Tissue-specific metabolism: the division of labor 892
Hormonal regulation of fuel metabolism 902
Obesity and the regulation of body mass 910
Information pathways
Chapter 24: Genes and chromosomes 923
Chromosomal elements 924
DNA supercoiling 930
The structure of chromosomes 938
Chapter 25: DNA metabolism 948
DNA replication 950
DNA repair 966
DNA recombination 978
Chapter 26: RNA metabolism 995
DNA-dependent synthesis of RNA 996
RNA processing 1007
RNA-dependent synthesis of RNA and DNA 1021
Chapter 27: Protein metabolism 1034
The genetic code 1034
Protein synthesis 1044
Protein targeting and degradation 1068
Chapter 28: Regulation of gene expression 1081
Principles of gene regulation 1082
Regulation of gene expression in procaryotes 1092
Regulation of gene expression in eukaryotes 1102
