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- ISBN-10 : 0716746840
- ISBN-13 : 978-0716746843
- Author:
With new co-authors Jeremy Berg and John Tymoczko, “Biochemistry” 5th edition has expanded integration of evolution, more chemical and structural insights, and a web based media component created simultaneously with the text. Improved pedagogy includes: chapter opening outlines, expanded end of chapter problem sets, new types of problems, and special icons highlighting evolutionary coverage, clinically relevant material, or related media content on the Web. “Biochemistry” also becomes the first text to fully reflect the revolution that has taken place in biomedical science in the past ten years, culminating in the human genome project. A key focus of the new edition is the unifying features of protein structure and function that have been revealed by the incredible progress in gene sequencing. All molecular diagrams have been recreated by Jeremy Berg for clearer and more consistent presentations of structure throughout, with the art programme being increased by nearly 20 per cent over the previous edition. The new author team has also worked to maintain the book’s defining feature: the characteristic clarity.
Table of contents:
Part 1 Foundations
1 The Chemical Basis of Life 1
1.1 What Is Biochemistry? 1
1.2 Biological Molecules 3
Cells contain four major types of biomolecules 3
There are three major kinds of biological polymers 6
Box 1.A Units Used in Biochemistry 7
1.3 Energy and Metabolism 10
Enthalpy and entropy are components of free energy 11
ΔG is less than zero for a spontaneous process 12
Life is thermodynamically possible 12
1.4 The Origin of Cells 14
Prebiotic evolution led to cells 15
Box 1.B How Does Evolution Work? 17
Eukaryotes are more complex than prokaryotes 17
The human body includes microorganisms 19
2 Aqueous Chemistry 27
2.1 Water Molecules and Hydrogen Bonds 27
Hydrogen bonds are one type of electrostatic force 29
Water dissolves many compounds 31
Box 2.A Why Do Some Drugs Contain Fluorine? 31
2.2 The Hydrophobic Effect 33
Amphiphilic molecules experience both hydrophilic interactions and the hydrophobic effect 35
The hydrophobic core of a lipid bilayer is a barrier to diffusion 35
Box 2.B Sweat, Exercise, and Sports Drinks 36
2.3 Acid–Base Chemistry 37
[H+] and [OH–] are inversely related 38The pH of a solution can be altered 39
Box 2.C Atmospheric CO2 and Ocean Acidification 39
A pK value describes an acid’s tendency to ionize 40
The pH of a solution of acid is related to the pK 41
2.4 Tools and Techniques: Buffers 44
2.5 Clinical Connection: Acid–Base Balance in Humans 46
Part 2 Molecular Structure and Function
3 Nucleic Acid Structure and Function 57
3.1 Nucleotides 57
Nucleic acids are polymers of nucleotides 58
Some nucleotides have other functions 60
3.2 Nucleic Acid Structure 61
DNA is a double helix 62
RNA is single-stranded 64
Nucleic acids can be denatured and renatured 64
3.3 The Central Dogma 67
Box 3.A Replication, Mitosis, Meiosis, and Mendel’s Laws 67
DNA must be decoded 70
A mutated gene can cause disease 71
Genes can be altered 72
Box 3.B Genetically Modified Organisms 73
3.4 Genomics 74
The exact number of human genes is not known 75
Genome size varies 75
Genomics has practical applications 77
Box 3.C Viruses 78
4 Protein Structure 86
4.1 Amino Acids, the Building Blocks of Proteins 86
The 20 amino acids have different chemical properties 88
Box 4.A Does Chirality Matter? 89
Box 4.B Monosodium Glutamate 91
Peptide bonds link amino acids in proteins 91
The amino acid sequence is the first level of protein structure 94
4.2 Secondary Structure: The Conformation of the Peptide Group 95
The α helix exhibits a twisted backbone conformation 96
The β sheet contains multiple polypeptide strands 96
Proteins also contain irregular secondary structure 98
4.3 Tertiary Structure and Protein Stability 99
Proteins can be described in different ways 99
Globular proteins have a hydrophobic core 100
Protein structures are stabilized mainly by the hydrophobic effect 101
Box 4.C Thioester Bonds as Spring-Loaded Traps 103
Protein folding is a dynamic process 103
Box 4.D Baking and Gluten Denaturation 104
Disorder is a feature of many proteins 105
Protein functions may depend on disordered regions 106
4.4 Quaternary Structure 107
4.5 Clinical Connection: Protein Misfolding and Disease 109
4.6 Tools and Techniques: Analyzing Protein Structure 111
Chromatography takes advantage of a polypeptide’s unique properties 111
Mass spectrometry reveals amino acid sequences 114
Box 4.E Mass Spectrometry Applications 116
Protein structures are determined by NMR spectroscopy, X-ray crystallography, and cryo-electron microscopy 116
5 Protein Function 125
5.1 Myoglobin and Hemoglobin: Oxygen-Binding Proteins 126
Oxygen binding to myoglobin depends on the oxygen concentration 127
Myoglobin and hemoglobin are related by evolution 128
Oxygen binds cooperatively to hemoglobin 129
A conformational shift explains hemoglobin’s cooperative behavior 130
Box 5.A Carbon Monoxide Poisoning 130
H+ ions and bisphosphoglycerate regulate oxygen binding to hemoglobin in vivo 132
5.2 Clinical Connection: Hemoglobin Variants 134
5.3 Structural Proteins 136
Actin filaments are most abundant 137
Actin filaments continuously extend and retract 138
Tubulin forms hollow microtubules 139
Keratin is an intermediate filament 142
Collagen is a triple helix 144
Box 5.B Vitamin C Deficiency Causes Scurvy 144
Collagen molecules are covalently cross-linked 145
Box 5.C Bone and Collagen Defects 147
5.4 Motor Proteins 148
Myosin has two heads and a long tail 148
Myosin operates through a lever mechanism 150
Kinesin is a microtubule-associated motor protein 151
Box 5.D Myosin Mutations and Deafness 151
Kinesin is a processive motor 152
5.5 Antibodies 154
Immunoglobulin G includes two antigen-binding sites 154
B lymphocytes produce diverse antibodies 156
Researchers take advantage of antibodies’ affinity and specificity 157
6 How Enzymes Work 167
6.1 What Is an Enzyme? 167
Enzymes are usually named after the reaction they catalyze 170
6.2 Chemical Catalytic Mechanisms 171
A catalyst provides a reaction pathway with a lower activation energy barrier 173
Enzymes use chemical catalytic mechanisms 173
Box 6.A Depicting Reaction Mechanisms 175
The catalytic triad of chymotrypsin promotes peptide bond hydrolysis 177
6.3 Unique Properties of Enzyme Catalysts 180
Enzymes stabilize the transition state 180
Efficient catalysis depends on proximity and orientation effects 181
The active-site microenvironment promotes catalysis 182
6.4 Chymotrypsin in Context 183
Not all serine proteases are related by evolution 183
Enzymes with similar mechanisms exhibit different substrate specificity 184
Chymotrypsin is activated by proteolysis 185
Protease inhibitors limit protease activity 186
6.5 Clinical Connection: Blood Coagulation 187
7 Enzyme Kinetics and Inhibition 198
7.1 Introduction to Enzyme Kinetics 198
7.2 Derivation and Meaning of the Michaelis–Menten Equation 201
Rate equations describe chemical processes 201
The Michaelis–Menten equation is a rate equation for an enzyme-catalyzed reaction 202
KM is the substrate concentration at which velocity is half-maximal 204
The catalytic constant describes how quickly an enzyme can act 204
kcat/KM indicates catalytic efficiency 205
KM and Vmax are experimentally determined 205
Not all enzymes fit the simple Michaelis–Menten model 207
7.3 Enzyme Inhibition 209
Some inhibitors act irreversibly 209
Competitive inhibition is the most common form of reversible enzyme inhibition 210
Transition state analogs inhibit enzymes 212
Other types of inhibitors affect Vmax 213
Box 7.A Inhibitors of HIV Protease 214
Allosteric enzyme regulation includes inhibition and activation 216
Several factors may influence enzyme activity 219
7.4 Clinical Connection: Drug Development 219
8 Lipids and Membranes 234
8.1 Lipids 234
Fatty acids contain long hydrocarbon chains 235
Box 8.A Omega-3 Fatty Acids 236
Some lipids contain polar head groups 237
Lipids perform a variety of physiological functions 239
Box 8.B The Lipid Vitamins A, D, E, and K 240
8.2 The Lipid Bilayer 241
The bilayer is a fluid structure 242
Natural bilayers are asymmetric 243
8.3 Membrane Proteins 244
Integral membrane proteins span the bilayer 245
An α helix can cross the bilayer 245
A transmembrane β sheet forms a barrel 246
Lipid-linked proteins are anchored in the membrane 246
8.4 The Fluid Mosaic Model 248
Membrane proteins have a fixed orientation 249
Lipid asymmetry is maintained by enzymes 250
9 Membrane Transport 258
9.1 The Thermodynamics of Membrane Transport 258
Ion movements alter membrane potential 259
Membrane proteins mediate transmembrane ion movement 260
9.2 Passive Transport 263
Porins are β barrel proteins 263
Ion channels are highly selective 264
Gated channels undergo conformational changes 265
Box 9.A Pores Can Kill 265
Aquaporins are water-specific pores 266
Some transport proteins alternate between conformations 268
9.3 Active Transport 269
The Na,K-ATPase changes conformation as it pumps ions across the membrane 269
ABC transporters mediate drug resistance 271
Secondary active transport exploits existing gradients 271
9.4 Membrane Fusion 272
SNAREs link vesicle and plasma membranes 273
Box 9.B Antidepressants Block Serotonin Transport 275
Endocytosis is the reverse of exocytosis 276
Autophagosomes enclose cell materials for degradation 277
Box 9.C Exosomes 278
10 Signaling 287
10.1 General Features of Signaling Pathways 287
A ligand binds to a receptor with a characteristic affinity 288
Most signaling occurs through two types of receptors 289
The effects of signaling are limited 290
10.2 G Protein Signaling Pathways 291
G protein–coupled receptors include seven transmembrane helices 292
The receptor activates a G protein 293
The second messenger cyclic AMP activates protein kinase A 294
Arrestin competes with G proteins 296
Signaling pathways must be switched off 296
The phosphoinositide signaling pathway generates two second messengers 297
Many sensory receptors are GPCRs 298
Box 10.A Opioids 299
10.3 Receptor Tyrosine Kinases 300
The insulin receptor dimer changes conformation 300
The receptor undergoes autophosphorylation 302
Box 10.B Cell Signaling and Cancer 303
10.4 Lipid Hormone Signaling 303
Eicosanoids are short-range signals 305
Box 10.C Inhibitors of Cyclooxygenase 306
11 Carbohydrates 315
11.1 Monosaccharides 315
Most carbohydrates are chiral compounds 316
Cyclization generates α and β anomers 317
Monosaccharides can be derivatized in many different ways 318
Box 11.A The Maillard Reaction 319
11.2 Polysaccharides 320
Lactose and sucrose are the most common disaccharides 321
Starch and glycogen are fuel-storage molecules 321
Cellulose and chitin provide structural support 322
Box 11.B Cellulosic Biofuel 323
Bacterial polysaccharides form a biofilm 324
11.3 Glycoproteins 325
Oligosaccharides are N-linked or O-linked 325
Oligosaccharide groups are biological markers 326
Box 11.C The ABO Blood Group System 327
Proteoglycans contain long glycosaminoglycan chains 327
Bacterial cell walls are made of peptidoglycan 328
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