v INTRODUCTION
1 Chemical Bonds and Energy Conservation
2 Thermodynamics and Energy Conservation
3 Potential Energy Curve
4 Redox States
5 Water, pH, Acid-Base Reactions, and Buffers
6 Structure of Water
7 Acid-Base Reactions
8 Concept of Acids and Bases in Relationship to pH
9 Buffers
10 Biomolecular Structures
11 Amino Acids and Proteins
12 Structure of Proteins
13 Primary Structure
14 Secondary Structure
15 a-Helix
16 ß-Pleated sheets
17 ß-Turns
18 Tertiary Structure
19 Quaternary Structure
20 Chemical and Enzymatic Reaction Mechanisms
21 Chemical Reaction Mechanisms
v BIOCHEMISTRY
1 First-Order Reactions
2 Second-Order Reactions
3 Some Factors That Influence Reaction Rates
4 Enzymatic Reaction Mechanisms
5 How Does an Enzyme Help Lower the Energy/Heat of Activation of a Reaction
6 Proximity and Orientation
7 Covalent Catalysis
8 Strain and Distortion
9 Acid-Base Catalysis
10 Selected List of Coenzymes and Their Roles in Catalysis
11 Classification of Enzymes by the Types of Reactions They Catalyze
12 Oxidoreductases
13 Transferases
14 Hydrolases
15 Lyases
16 Isomerases
17 Ligases
18 Enzyme Kinetics
19 Practical Aspect of Initial Velocity Measurement
20 Lineweaver-Burk Plots
21 Diagnostic Value of Lineweaver-Burk Plots: Enzyme Inhibition
22 Classification of the Types of Enzyme Inhibitors
23 Mechanism-Based Inhibitors
24 Two-Substrate Reactions
25 Sequential Reactions May Be Either Random or Ordered
26 Ping-Pong or Double-Displacement Reactions
27 Antibodies as Catalysts
28 Regulation of Enzymatic Activity
29 Summary of Regulatory Mechanisms
30 Kinetic Models for Allosteric Regulation
31 Kinetic Description of Allosteric Interactions: The Concerted Model
32 Significance of the Hill Coefficient
33 Metabolism
34 Forms of Conserved Energy in Metabolism
35 Glycolysis
36 Reaction That Commits Glucose Metabolism to Glycolysis
37 Aldolase Catalyzes the Production of Two -Carbon
38 Compounds from Fru ,-P
39 Triose Phosphate Isomerase
40 Glyceraldehyde -Phosphate Dehydrogenase (GAPDH) Reaction
41 Phosphoglycerate Kinase Reaction
42 Phosphoglycerate Mutase Reaction
43 Enolase Catalyzes the Second “High-Energy” Compound in Glycolysis
44 Pyruvate Kinase Generates the Second ATP Molecule in Glycolysis
45 Summary of Glycolysis
46 Pyruvate Metabolism: Formation of Acetylcoenzyme A
47 The Tricarboxyclic Acid Cycle (TCA Cycle)
48 Regulation of the TCA cycle
49 Anaplerotic Reactions for the TCA Cycle
50 Oxidative Phosphorylation
51 Pentose Phosphate Pathway
52 Oxidative Phase of the Pentose Phosphate Pathway
53 Nonoxidative Phase of the Pentose Phosphate Pathway
54 Glucuronic Acid Oxidative Pathway
55 Gluconeogenesis and Glycogenesis
56 Summary of Entry Points in the TCA Cycle
57 and Glycolysis That Can Lead to Gluconeogenesis
58 Glycogen Metabolism
59 Glycogenesis
60 Glycogenolysis
61 Regulation of Glycogen Metabolism
62 Photosynthesis
63 Photochemical Consideration of Light Absorption and Energy Generation
64 Light Independent Reactions of Photosynthesis: The Calvin Cycle
65 Adaptive Photosynthetic Mechanisms
66 Nitrogen Metabolism
67 Nitrogen Fixation
68 Chemical Reactions of Pyridoxyl Phosphate Relative to Amino Acid Metabolism
69 Biosynthesis of Amino Acids
70 Amino Acids Derived from Oxaloacetate/Aspartate
71 Amino Acids Derived from -Phosphoglycerate
72 Cysteine
73 Serine
74 Glycine
75 Amino Acids Derived from Pyruvate
76 Amino Acids Derived from a-Ketoglutarate
77 Amino Acids Derived from Phosphoenolpyruvate and Erythrose--phosphate
78 Histidine
79 Degradation of Amino Acids
80 Methionine
81 The Urea Cycle
82 Nucleotide Structure and Metabolism
83 Synthesis of Purines
84 Summary of Key Points About Purine Biosynthesis
85 Degradation of Purines
86 Synthesis of Pyrimidines
87 Synthesis of Deoxyribonucleotides
88 Regulation of Ribonucleotide Reductase Activity
89 Thymine Biosynthesis
90 Degradation of Pyrimidines
91 Heme Metabolism
92 Heme and Chlorophyll Biosynthesis
93 Heme and Chlorophyll Degradation
94 Lipid Metabolism
95 Fatty Acid Biosynthesis
96 Elongation of Palmitic Acid
97 Formation of Unsaturated Fatty Acids
98 Nomenclature and Other Positions Where Desaturases Function
99 Arachiodonic Acid and Signaling/Regulatory Molecules
100 Cholesterol and Steroid Hormones Are Derived from Acetate
101 Fatty Acids Are Stored as Triglycerides
102 Sphingolipids
103 Fatty Acid Oxidation
104 Special Cases to Consider for b-Oxidation of Fatty Acids
105 Methods
106 Methods for Cell Disruption
107 Mechanical Methods
108 Nonmechanical Methods of Cell Disruption
109 Separation of Cellular Components by Centrifugation
110 Centrifugal Force Required to Pellet Selected Cellular Components
111 Purification of Soluble Proteins
112 Chromatography
113 Ion Exchange Chromatography
114 Hydrophobic Interaction Chromatography
115 Gel Filtration Chromatography
116 Two-Dimensional Gel Electrophoresis
117 Determination of Molecular Mass Using SDS Denaturing Gels
118 Western Blot Analysis
119 Cellular Compartments of Prokaryotes and Eukaryotes
120 Organization, Dynamics, and Functions
121 Microscopy
122 General Introduction to Prokaryotes and Eukaryotes
123 Prokaryotes
124 Eukaryotes
125 Cell Death
126 Apoptosis
127 Necrosis
128 Cellular Membrane Systems (Structure and Transport)
129 Prokaryotic Cells, Plasma Membrane, and Cell Wall
130 Eukaryotic Plasma Membranes and Cell Walls
131 Membrane Biogenesis
132 Membrane Transport
133 Inactive Transport
134 Active Transport
135 Exo- and Endocytosis
v CELL BIOLOGY
1 Nucleus (Envelope and Matrix) and Chromosomes
2 Prokaryotic Cells—Chromosome
3 Eukaryotic Cells—Chromosomes and Nucleus
4 Other Intracellular Structures, Including Mitochondria and Chloroplasts
5 Prokaryotes
6 Eukaryotes
7 Specialized Structures and Other Characteristics
8 Cell Dynamics
9 Cell Surface and Cell Communication
10 Extracellular Matrix
11 The Extracellular Matrix of Connective Tissue
12 Connective Tissue
13 The Proteins of Connective Tissue
14 The Extracellular Matrix of Endothelial Tissue
15 Cell–Cell Interaction
16 Binding of Cells to the Extracellular Matrix
17 Communication between Extracellular Matrix and Cytoskeleton
18 Cell Adhesion and Junctions: Cell–Cell Communication
19 Signal Transduction and Receptor Function
20 Cell Membrane Receptors
21 Second Messenger Systems
22 The
23 The Phosphatidylinositol Pathway
24 G-Protein-Associated Ion Channels
25 Receptors That Are Enzymes
26 Steroid and Thyroid Hormones
27 Excitable Membrane Systems
28 Cytoskeleton, Motility, and Shape
29 Actin Filaments
30 Actin in Muscle Contraction
31 Microtubules
32 Intermediate Filaments
33 Organization of the Cytoskeleton
34 Cell Surface Structures of Prokaryotes
35 Protein Synthesis and Processing
36 Cell Division, Differentiation, and Development
37 Bacterial Cell Division
38 Eukaryotic Cell Cycle
39 Mitosis and Cytokinesis
40 Cytokinesis
41 Growth Factors
42 Meiosis and Gametogenesis
43 Fertilization and Early Embryonic Development
44 Fertilization
45 Embryogenesis
46 Early Mammalian Development
47 From Gastrula to Fully Developed Organism
48 Positional Information
49 Nuclear/Cytoplasmic Interactions
50 Tissue-Specific Expression
v MOLECULAR BIOLOGY
1 Mendelian and Non-Mendelian Inheritance
2
3 Transformation, Transduction, and Conjugation
4 Recombination and Complementation
5 Mutational Analysis
6 Genetic Mapping and Linkage Analysis
7 Chromatin and Chromosomes
8 Karyotypes
9 Translocations, Inversions, Deletions, and Duplications
10 Aneuploidy and Polyploidy
11 Structure
12 Genomics
13 Genome Structure
14 Repeated DNA and Gene Families
15 Centromeres and Telomeres
16 Gene Identifi cation
17 Transposable Elements
18 Gene Maintenance
19 DNA Replication
20 The Challenges of DNA Replication
21 DNA Damage and Repair
22 DNA Modifi cation
23 DNA Recombination and Gene Conversion
24 Branch Migration
25 Gene Conversion
26 The Genetic Code
27 Transcription
28 Gene Regulation in Prokaryotes
29 Positive and Negative Control of the Operon
30 Gene Regulation in Eukaryotes
31 Cis- and Trans-Acting Regulatory Elements
32 Gene Rearrangements and Amplifi cation
33 Bacteriophages and Animal and Plant Viruses
34 Genome Replication and Regulation
35 Virus-Host Interactions
36 Methodology
37 Restriction Maps
38 DNA Cloning in Prokaryotes and Eukaryotes
39 Other Uses of Restriction Endonucleases
40 Nucleic Acid Blotting and Hybridization
41 PCR
42 Sequencing and Analysis
43 Protein-Nucleic Acid Interaction
44 Site-Directed Mutagenesis
45 Answer to Mapping Problem
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