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Basic Concepts in Biochemistry A Student's Survival Guide 2d ed - Hiram F. Gilbert

Contents


CHAPTER 1 WHERE TO START 1
Instructions 1
What Do I Need to Know? 2
Instructions for Use 2
Studying and Exams 2
Trivia Sorter 4

CHAPTER 2 PROTEIN STRUCTURE 6
Amino Acid Structure 6
Interactions 8
Water 9
Hydrophobic Interaction 9
van der Waals Interactions and London Dispersion Forces 11
Hydrogen Bonds 11
Secondary Structure 12
Protein Stability 15
Favorable (Good) Interactions 17
Unfavorable (Bad) Interactions 17
Temperature-Sensitive Mutations 19
Ligand-Binding Specificity 20
Global Conclusion 21
CHAPTER 3 MEMBRANES AND
MEMBRANE PROTEINS 22
General Membrane Function 22
Membrane Composition 23
Phospholipid Bilayer 24
Membrane Structure 25
Posttranslational Modification 26
Membrane Fluidity 27
Diffusion in Membranes 28
Movement of Ions and Molecules Across Membranes 28

Transport Across Membranes 29
The Nernst Equation 31
CHAPTER 4 DNA-RNA STRUCTURE 35
DNA Structure 35
DNA Stability 37
RNA Secondary Structure 38
CHAPTER 5 EXPRESSION OF GENETIC
INFORMATION 40
Information Metabolism 40
Directions and Conventions 41
DNA Replication 42
Types of DNA Polymerase 45
Recombination 47
Regulation of Information Metabolism 49
Transcription 53
Regulation of Transcription 55
Translation 57
Use of High-Energy Phosphate Bonds During Translation 60
CHAPTER 6 RECOMBINANT-DNA METHODOLOGY 61
Restriction Analysis 61
Gels and Electrophoresis 65
Blotting 67
Restriction Fragment-Length Polymorphism 69
Cloning 70
Sequencing 73
Mutagenesis 75
Polymerase Chain Reaction 76
CHAPTER 7 ENZYME MECHANISM 80
Active Site 81
Transition State 81
Catalysis 83
Lock and Key 83
Induced Fit 83
Nonproductive Binding 85
Entropy 87
Strain and Distortion 88

Transition-State Stabilization 88
Transition-State Analogs 91
Chemical Catalysis 93
CHAPTER 8 ENZYME KINETICS 95
S, P, and E (Substrate, Product, Enzyme) 96
Amounts and Concentrations 96
Active Site 97
Assay 98
Velocity 98
Initial Velocity 100
Mechanism 101
Little k’s 102
Michaelis-Menten Equation 103
Vmax 106
kcat 106
Km 107
Special Points 107
kcat/Km 107
Rate Accelerations 108
Steady-State Approximation 109
Transformations and Graphs 111
Inhibition 112
Allosterism and Cooperativity 117
The Monod-Wyman-Changeaux Model 119
CHAPTER 9 SIGNAL TRANSDUCTION PATHWAYS 123
Signal Transduction Pathways 123
Organization 124
Signals 125
Receptors 126
Soluble Receptors 126
Transmembrane Receptors 128
Enzyme Coupled Receptors 128
G-Protein Coupled Receptors 131
Ion-Channel Coupled Receptors 132
Second Messengers 133
Amplifiers 136
Integrators 137
Inhibitors 138

CHAPTER 10 GLYCOLYSIS
AND GLUCONEOGENESIS 141
Glycolysis Function 143
Glycolysis Location 143
Glycolysis Connections 143
Glycolysis Regulation 143
Glycolysis ATP Yields 144
Glycolysis Equations 144
Effect of Arsenate 144
Lactate or Pyruvate 145
Gluconeogenesis Function 145
Gluconeogenesis Location 145
Gluconeogenesis Connections 145
Gluconeogenesis Regulation 146
Gluconeogenesis ATP Costs 146
Gluconeogenesis Equations 146
CHAPTER 11 GLYCOGEN SYNTHESIS
AND DEGRADATION 147
Function 147
Location 147
Connections 148
Regulation 148
ATP Yield 150
ATP Cost 150
Molecular Features 150
CHAPTER 12 TCA CYCLE 153
TCA Cycle 153
CHAPTER 13 FAT SYNTHESIS
AND DEGRADATION 155
Fatty Acid Synthesis Function 156
Fatty Acid Synthesis Location 156
Fatty Acid Synthesis Connections 157
Fatty Acid Synthesis Regulation 157
Fatty Acid Synthesis ATP Costs (for C16) 157
Fatty Acid Synthesis Equation 159
Elongation and Desaturation 160
Triglyceride and Phospholipid Synthesis 162

-Oxidation Function 164
-Oxidation Location 164
Carnitine Shuttle 164
-Oxidation Connections 164
-Oxidation Regulation 164
-Oxidation ATP Yield 166
-Oxidation Equation 167
-Oxidation of Unsaturated Fatty Acids 168
-Oxidation of Odd-Chain-Length Fatty Acids 172
CHAPTER 14 ELECTRON TRANSPORT
AND OXIDATIVE PHOSPHORYLATION 173
Oxidation and Reduction 173
The Electron Transport Chain 174
Connections 176
Regulation 178
P/O Ratios 178
Uncouplers 179
Inhibitors 180
CHAPTER 15 PENTOSE PHOSPHATE
PATHWAY 183
Pentose Phosphate Pathway 183
CHAPTER 16 AMINO ACID METABOLISM 186
Nonessential Amino Acid Synthesis 186
Essential Amino Acids 187
Amino Acid Degradation 187
Generalities of Amino Acid Catabolism 187
Products of Amino Acid Degradation 188
CHAPTER 17 INTEGRATION OF ENERGY
METABOLISM 190
Integrating Metabolic Pathways 191
ATP 192
Glucose 192
Storage Molecules 193
Metabolic States and Signals 194
Insulin 195

Glucagon 196
Epinephrine 197
Secondary Signals 198
Generalities of Metabolism 199
Phosphorylation 202
Glycogen 204
Metabolic Movements of Glycogen 205
Fat 207
Metabolic Movements of Fat 207
Protein 209
Metabolic Movements of Protein 209
Tissue Cooperation 211
Liver 212
Muscle 212
Adipose 212
Brain 213
Connection of Storage Pools 213
Feeding 214
Fasting 214
Starvation 217
Excitement 219
Interorgan Cycles 221
Cori Cycle 221
Alanine Cycle 222
Ketone Bodies 223
CHAPTER 18 UREA CYCLE 225
Urea Cycle 225
CHAPTER 19 PURINE METABOLISM 227
Purine Synthesis 227
Purine Salvage 228
Deoxynucleotides 228
Purine Degradation 229
CHAPTER 20 PYRIMIDINE METABOLISM 230
Pyrimidine Synthesis 230
Pyrimidine Salvage 231
Pyrimidine Degradation 232

CHAPTER 21 ONE-CARBON METABOLISM 233
One-Carbon Metabolism 233
Oxidation States of Carbon 233
CHAPTER 22 TRACKING CARBONS 236
Glucose to Pyruvate 236
TCA Cycle 238
CHAPTER 23 ph, pKA, pROBLEMS 241
Proton: H or H3O 242
Acid 242
Base 242
Not All Acids and Bases Are Created Equal 243
pKa log (Ka) 244
Weak Acids Make Strong Bases (and Vice Versa) 244
Who Gets the Proton? 245
Don’t Forget Stoichiometry 245
The Sadistic Little p 246
Taking log10(x) 247
Taking log10(x) 247
pH log10 [H ] 248
pKa log10 (Ka) 248
Buffers 248
Henderson-Hasselbalch Equation 249
Titration Curves 250
pI—Isoelectric Point 254
The Bicarbonate Buffer 255
Imbalance in Blood pH 257
Acidosis and Alkalosis 258
CHAPTER 24 THERMODYNAMICS
AND KINETICS 261
Thermodynamics 261
Free Energy 263
Adding Free-Energy Changes 268
Coupling Free Energies 268
Thermodynamic Cycles 269
G H T S 272
Driving Force 273

Kinetics 275
Velocity 275
Transition State Theory 276
Rate Constants 277
Rate Constants and Mechanism 283

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