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PART Ⅰ:STRUCTURE AND FUNCTION OF BIOMACROMOLECULE 1

Chapter 1 Structure and Function of Protein 1

SECTION 1 THE COMPOSITION OF PROTEIN 2

1.1 Amino acid 2

1.2 Peptide 5

1.3 Some small polypeptides have biological activity 6

SECTION 2 MOLECULAR STRUCTURE OF PROTEINS 7

2.1 Primary structure 7

2.2 Secondary structure 7

2.3 Tertiary structure 11

2.4 Major noncovalent bond 12

2.5 Quaternary structure 13

SECTION 3 RELATION BETWEEN STRUCTURE AND FUNCTION OF PROTEINS 14

3.1 Primary structure and potential function of protein 14

3.2 Spatial structure shows the function of protein 15

SECTION 4 CHEMICAL AND PHYSICAL PROPERTIES OF PROTEINS 19

4.1 Ultraviolet absorption spectrum of protein 19

4.2 Isoelectric point(pI) 19

4.3 Denaturation of protein 20

SECTION 5 ISOLATION,PURIFICATION AND SEQUENCING OF PROTEINS 21

5.1 Dialysis and ultrafiltration 21

5.2 Precipitation with acetone,salting precipitation and immunoprecipitation 21

5.3 Chromatographic separations 23

5.4 Electrophoresis 24

5.5 Ultracentrifugation 26

SUMMARY 27

Chapter 2 Chemistry of Nucleic Acids 29

SECTION 1 MOLECULAR COMPOSITION OF NUCLEIC ACIDS 30

1.1 Basic components 30

1.2 Nucleosides 32

1.3 Mononucleotides 32

SECTION 2 MOLECULAR STRUCTURES OF DNA 33

2.1 Primary structure of nucleic acid 33

2.2 Chargaff's rules 34

2.3 Secondary structure of DNA 35

SECTION 3 PHYSICO-CHEMICAL PROPERTIES OF NUCLEIC ACIDS 37

3.1 Viscosity 37

3.2 Ultraviolet absorption 37

3.3 Denaturation and renaturation of DNA 37

3.4 Hydrolysis of acid or alkali 40

SECTION 4 STRUCTURES OF RNA 40

4.1 Messenger RNA 40

4.2 Transfer RNA 41

4.3 Ribosomal RNA 42

SUMMARY 44

Chapter 3 Enzymes 45

SECTION 1 THE MOLECULAR COMPOSITION AND FUNCTION OF ENZYMES 46

1.1 The molecular composition of enzymes 46

1.2 The active center of enzymes 47

1.3 Many enzymes require cofactors 48

SECTION 2 PROPERTIES AND MECHANISM OF ENZYME CATALYSIS 50

2.1 Remarkable properties of enzymes 50

2.2 Mechanism of enzyme catalysis 52

SECTION 3 THE KINETICS OF ENZYME CATALYSIS 54

3.1 Catalysis occurs at the active site 54

3.2 Multiple factors affect the rates of enzyme-catalyzed reactions 57

3.3 Initial rate is proportionate to enzyme concentration 59

3.4 Substrate concentration affects reaction rate 59

3.5 The Michaelis-Menten equations model the effects of substrate concentration 60

3.6 Kinetic analysis distinguishes competitive from noncompetitive inhibition 62

SECTION 4 ZYMOGENS AND ISOZYMES 65

4.1 Zymogens and zymogen activation 65

4.2 Isozymes are physically distinct forms of the same catalytic activity 66

SECTION 5 THE NAME AND CLASSIFICATION OF ENZYMES 68

SECTION 6 THE QUANTITATIVE ANALYSIS OF CERTAIN PLASMA ENZYMES IS OF DIAGNOSTIC SIGNIFICANCE 69

6.1 Low levels of nonfunctional plasma enzymes result from normal destruction of cells 69

6.2 Nonfunctional plasma enzymes aid diagnosis and prognosis 69

SUMMARY 70

PART Ⅱ:METABOLISM 73

Chapter 4 Metabolism of Carbohydrate 73

SECTION 1 DIGESTION OF DIETARY CARBOHYDRATES 74

SECTION 2 GLYCOLYSIS 75

2.1 Concept of glycolysis 75

2.2 Glycolytic pathway 75

2.3 Regulation of glycolysis 79

2.4 Lactate metabolism 82

SECTION 3 THE PYRUVATE DEHYDROGENASE COMPLEX AND THE CITRIC ACID CYCLE 83

3.1 The pyruvate dehydrogenase complex 83

3.2 Regulation of the PDH complex 84

3.3 Reactions of the tricarboxylic acid cycle 85

SECTION 4 PENTOSE PHOSPHATE PATHWAY 90

4.1 Reactions of the pentose phosphate pathway 90

4.2 The functions of this pathway 93

4.3 Erythrocytes and the pentose phosphate pathway 94

4.4 Pentose phosphate pathway with disease 94

SECTION 5 GLYCOGEN METABOLISM 95

5.1 Glycogen synthesis 95

5.2 Glycogenolysis 97

5.3 The functions of glycogenesis and glycogenolysis 99

SECTION 6 GLUCONEOGENESIS 99

6.1 Gluconeogenesis 100

6.2 Regulation of gluconeogenesis 103

SECTION 7 REGULATION OF BLOOD SUGAR LEVELS 104

SUMMARY 105

Chapter 5 Biological Oxidation 107

SECTION 1 THE WAY OF OXIDATION 107

1.1 Addition of oxygen 107

1.2 Removal of electrons 107

1.3 Dehydrogenation 108

SECTION 2 RESPIRATORY CHAIN 108

2.1 The composition of respiratory chains 110

2.2 Two capital kinds of respiratory chains 113

2.3 Oxidative phosphorylation 121

2.4 Factors of influence on oxidative phosphorylation 129

2.5 Shuttle systems are required for mitochondrial oxidation of cytosolic NADH 132

SUMMARY 134

Chapter 6 Lipid Metabolism 136

SECTION 1 DIGESTION AND ABSORPTION OF LIPIDS 137

SECTION 2 BLOOD LIPIDS AND LIPOPROTEINS 138

2.1 The composition and content of blood lipoprotein 138

2.2 The classification of lipoproteins 140

SECTION 3 INTERMEDIATE METABOLISM OF TRIACYLGLYCEROLS 141

3.1 Hydrolysis of triacylglycerols in adipose tissue 142

3.2 Oxidation of fatty acids 143

3.3 Fatty acid synthesis 148

3.4 Biosynthesis of triacylglycerol 150

SECTION 4 METABOLISM OF PHOSPHOLIPIDS 152

SECTION 5 CHOLESTEROL METABOLISM 154

5.1 Biosynthesis of cholesterol 155

5.2 Transformation and excretion of cholesterol 156

SUMMARY 157

Chapter 7 Amino Acid Metabolism 159

SECTION 1 NUTRITION OF PROTEINS 159

1.1 Nutrition of the proteins 159

1.2 Nitrogen balance and protein requirements 160

1.3 The biosynthetic pathways of amino acids 161

SECTION 2 DIGESTION AND ABSORPTION OF PROTEINS 162

2.1 Protein tumover occurs in all forms of life 162

2.2 Proteases and peptidases degrade proteins to amino acids 163

SECTION 3 AMINO ACID CATABOLISM 165

3.1 Overall view 165

3.2 Deamination of amino acids 165

3.3 Metabolism of the carbon skeletons of amino acids 168

SECTION 4 METABOLISM OF AMMONIA 170

4.1 Sources and disposals of blood ammonia 170

4.2 Transport of ammonia 170

4.3 Inter-organ exchange maintains circulating levels of amino acids 172

4.4 Biosynthesis of urea 172

4.5 Metabolic disorders are associated with each reaction of the urea cycle 176

SECTION 5 CONVERSION OF AMINO ACIDS TO SPECIALIZED PRODUCTS 178

5.1 Glycine participates in biosynthesis of glycine conjugates,creatine,heme,and purines 178

5.2 α-Alanine is a major plasma amino acid 179

5.3 Mammals catabolize β-alanine via malonate semialdehyde 179

5.4 S-adenosylmethionine provides methyl groups for biosynthesis 179

5.5 Urinary sulfate derives from cysteine 180

5.6 Decarboxylation of histidine forms histamine 180

5.7 Omithine and hence arginine form polyamines 180

5.8 Tryptophan forms serotonin 182

5.9 Melanins are polymers of tyrosine catabolites 184

5.10 Creatinine excretion is a function of muscle mass 186

5.11 Formation and catabolism of γ-aminobutyrate 186

SUMMARY 187

Chapter 8 Nucleotide Metabolism 189

SECTION 1 METABOLISM OF PURINE NUCLEOTIDES 190

1.1 Biosynthesis of purine nucleotides 190

1.2 Degradation of purines leads to uric acid 194

1.3 Clinical significances of purine metabolism 195

SECTION 2 METABOLISM OF PYRIMIDINE NUCLEOTIDES 196

2.1 Pyrimidine nucleotide biosynthesis 196

2.2 Salvage pathways of pyrimidine 199

2.3 Clinical significances of pyrimidine metabolism 200

SUMMARY 201

PART Ⅲ:GENE EXPRESSING 203

Chapter 9 DNA Replication 203

SECTION 1 PROKARYOTIC DNA SYNTHESIS 204

1.1 Separation of the two complementary DNA strands 205

1.2 Formation of the replication fork 205

1.3 Direction of DNA replication 207

1.4 RNA primer 208

1.5 Chain elongation 209

1.6 Excision of RNA primers and their replacement by DNA polymerase Ⅰ 211

1.7 DNA ligase 213

SECTION 2 EUKARYOTIC DNA REPLICATION 213

2.1 The eukaryotic cell cycle 213

2.2 Eukaryotic DNA polymerases 214

2.3 Telomerase 214

2.4 Reverse transcriptase 215

2.5 Inhibition of DNA synthesis by nucleoside analogs 216

2.6 Organization of eukaryotic DNA 216

SECTION 3 DNA REPAIR 218

3.1 Strand-directed mismatch repair system 218

3.2 Repair of damage caused by ultraviolet light 219

3.3 Correction of base alterations 219

3.4 Repair of double-strand breaks 220

SUMMARY 221

Chapter 10 RNA Synthesis 223

SECTION 1 TEMPLATES AND ENZYMES 225

1.1 Asymmetric transcription 225

1.2 DNA-dependent RNA polymerase 225

SECTION 2 THE PROCESS OF TRANSCRIPTION 227

2.1 Initiation 228

2.2 Elongation 232

2.3 Termination 233

2.4 Action of antibiotics 234

SECTION 3 POST TRANSCRIPTIONAL MODIFICATION OF RNA 235

3.1 mRNA processing 236

3.2 Ribosomal RNAs and tRNAs also undergo processing 241

3.3 tRNA processing 242

SUMMARY 243

Chapter 11 Protein Synthesis 245

SECTION 1 GENETIC CODE 246

1.1 Codon 247

1.2 Characteristics of the genetic code 248

1.3 Consequences of altering the nucleotide sequence 249

SECTION 2 COMPONENTS REQUIRED FOR TRANSLATION 249

2.1 Amino acids 250

2.2 Transfer RNA 250

2.3 Aminoacyl-tRNA synthases 251

2.4 Messenger RNA 251

2.5 Functionally competent ribosomes 251

2.6 Protein factors 252

2.7 ATP and GTP are required as sources of energy 252

SECTION 3 THE PROCESS OF PROTEIN SYNTHESIS 253

3.1 Activation of amino acids:Formation of aminoacyl-tRNA 253

3.2 The process of translation 254

3.3 Polysomes 260

SECTION 4 POSTTRANSLATIONAL MODIFICATION OF POLYPEPTIDE CHAIN 261

4.1 Trimming 261

4.2 Covalent alterations 262

4.3 Clinical relatives in protein synthesis 263

SECTION 5 REGULATION AND CONTROL OF GENE EXPRESSION 265

5.1 Gene control in prokaryotes 266

5.2 Gene control in eukaryotes 269

SUMMARY 270

PART Ⅳ:SPECIAL TOPICS 273

Chapter 12 Biochemistry of Liver 273

SECTION 1 THE STRUCTURAL FEATURE OF LIVER 273

SECTION 2 THE IMPORTANT ROLE OF LIVER IN MATERIAL METABOLISM 274

2.1 Carbohydrate metabolism 275

2.2 Protein metabolism 275

2.3 Lipid metabolism 276

2.4 Storage and filtering of blood 276

2.5 Removal of used hormones and cholesterol from the blood 276

2.6 Making bile salts 276

2.7 Destruction of any bacteria,bowel toxins and so on 277

SECTION 3 FUNCTIONS OF BIOTRANSFORMATION OF LIVER 277

3.1 Hydroxylation 278

3.2 Reduction reaction 280

3.3 Lytic response 280

3.4 Conjugation reactions 280

SECTION 4 METABOLISMS OF BILE ACID 282

4.1 Primary bile acids and biosynthesis of bile acids 283

4.2 Secondary bile acids and enterohepatic circulation of the bile salts 284

4.3 Regulation of bile acid synthesis 285

4.4 Clinical significance of bile acid synthesis 285

SECTION 5 METABOLISMS OF BILE PIGMENTS 286

5.1 Catabolism of heme 287

5.2 The liver takes up bilirubin 289

5.3 Hyperbilirubinemia causes jaundice 290

SUMMARY 292

Chapter 13 Biochemistry of Blood 293

SECTION 1 PLASMA PROTEINS 293

1.1 The composition of blood 293

1.2 The blood has many functions 294

1.3 Plasma contains a complex mixture of proteins 294

SECTION 2 RED BLOOD CELLS 300

2.1 Metabolic characteristics of mature erythrocytes 300

2.2 Biosynthesis of heme 303

SUMMARY 307

Chapter 14 Recombinant DNA Technology 309

SECTION 1 DNA CLONING 309

1.1 Cutting and joining DNA 310

1.2 Vectors 313

1.3 Transformation 315

1.4 Screening 315

SECTION 2 CLONING A GENE 317

2.1 Genomic library 317

2.2 cDNA library 318

2.3 PCR 320

2.4 Chemical synthesis 325

SECTION 3 IDENTIFYING DNA SEQUENCE 325

3.1 Probes 325

3.2 Gel electrophoresis 326

3.3 Nucleic acid hybridization 327

3.4 DNA sequencing 329

SECTION 4 MANIPULATING GENE EXPRESSION 330

4.1 Expression of cloned genes in bacteria 330

4.2 Expression of cloned genes in eukaryotic host cells 332

4.3 Protein purification 334

4.4 Alterations in cloned genes produce 335

SECTION 5 MEDICAL APPLICATIONS OF RECOMBINANT DNA TECHNOLOGY 336

5.1 The analysis of gene variations 336

5.2 Gene therapy 337

5.3 Transgenic animals 338

SUMMARY 338

The Confer of Special Term with Frequently Used 340