Contents

Preface
Acknowledgements
About the Authors

Chapter 1:- Biochemistry in Space and Time
1.1 Biochemical Unity Underlies Biological Diversity
1.2DNA Illustrates the Interplay between form and Function
1.3 Concepts from Chemistry Explain the Properties of Biological Molecules
1.4 DNA Sequencing is Transforming Biochemistry, Medicine and other Fields
1.5 Biochemistry is an Interconnected Human Endeavor

Chapter 2:- Protein Composition and Structure
2.1 Several Properties of Proteins Structure
2.2 Proteins are Built from a Repertoire of 20 Amino Acids
2.3 Primary Structure Amino Acids are Linked by Peptide Bonds to Form Polypeptide Chains
2.4 Secondary Structure: Polypeptide Chains can Fold into regular Structures
2.5 Tertiary Structure: Proteins Can Fold into Globular or Fibrous Structures
2.6 Quaternary Structure: Polypeptide Chains can Assemble into multi-subunit structures
2.7 The Amino Acid Sequence of a Proteins

Chapter 3:- Binding and Molecular Recognition
3.1 Binding is a Fundamental Process in Biochemistry
3.2 Myoglobin is an Efficient Oxygen
3.3 Hemoglobin is an Efficient Oxygen Carrier
3.4 The Immune System Depends on Key Binding Proteins
3.5 Quantitative Terms Can Describe Binding Propensity


Chapter 4:- Protein Methods
4.1 The Purification of Proteins is an Essential First Step in Understanding Their Function
4.2 Immunology Provides important Techniques to Investigating Proteins
4.3 Mass Spectrometry is a powerful technique
4.4 Peptides can be Synthesized by Automated Solid Phase Methods
4.5 Three Dimensional Protein Structures can be Determined Experimentally

Chapter 5:- Enzymes: Core Concepts and Kinetics
5.1 Enzymes are powerful and highly Specific Catalysts
5.2 Gibbs Free Energy is a useful Thermodynamic Function
5.3 Enzymes Accelerate Reactions by Facilitating the Formation of the Transition State

Chapter 6:- Enzymes Catalytic Strategies
6.1 Enzymes use a Core Set of Catalytic Strategies
6.2 Proteases Facilitate a Fundamentally Difficult Reaction
6.3 Carbonic Anhydrases make a fast Reaction Faster
6.5 Molecular Motor Proteins Harness changes in Enzymes

Chapter 7:- Enzyme Regulatory Strategies
7.1 Allosteric Regulation Enables Control of Metabolic Pathways
7.2 Isozymes Provide a means of regulation
7.3 Covalent Modification is a Means of Regulating Enzyme Activity
7.4 Many Enzymes are activated by specific Proteolytic Cleavage
7.5 Enzymatic Cascades Allow Rapid Responses Such as Blood Clotting

Chapter 8:- DNA, RNA and the Flow of Genetic Information
8.1 A Nucleic Acid consists of Four Kinds
8.2 A pair of Nucleic Acid Stands with Complementary Sequences
8.3 The Double Helix Facilitates the Accurate Transmission of Heredity Information
8.4 DNA is replicated by polymerases that take Instructions from Templates
8.5 Gene Expression is the Transformation of DNA Information into Functional Molecules

Chapter 9 :- Nucleic Acid Methods
9.1 The Exploration of Genes Relies on Key Tools
9.2 Recombinant DNA Technology has Revolutionized All aspects of Biology
9.3 Complete Genomes have been sequenced and analyzed
9.4 Eukaryotic Genes can be Quantitated and Manipulated with Considerable Precision

Chapter 10:- Exploring Evolution and Bioiformatics
10.1 Homologs are Descended from a Common Ancestor
10.2 Examination of Three Dimensional Structure Enhances our Undestanding of Evolutionary Relationships
10.3 Evolutionary Trees can be Constructed on the basis of Sequence Information
10.4 Lectins are Specific Carbohydrate-Binding Proteins

Chapter 12:- Lipid and Biological Membranes
12.1 Fatty Acids are Key Constituents of Lipids
12.2 Biological Membranes are composed of Three Common types of Membranes Lipids
12.3 Phospholipids and Glycolipids Readily form Bimolecular Sheets in Aqueos Media

Chapter 13:- Membrane Channels and Pumps
13.1 The Transport of Molecules Across a Membrane
13.2 Two Families of Membrane Protiens Use ATP Hydrolysis to actively Transport Ions and Molecules Across membranes
13.3 Lactose Permease is an Archetype of Secondary Transporters
13.4 Specific Channels can rapidly transport Ions Across Membranes
13.5 GAP ?Junctions Allow Ions and Small Molecules to Flow between Communicating Cells

Chapter 14:- Signals - Transduction Pathways
14.1 Many Signals - Transduction Pathways share common Themes
14.2 Epinephrine Signaling Heterotrimeric G Proteins Transmit Signals and Reset Themselves
14.3 Insulin Signaling: Phosphorylation Cascades are Central to Many Transduction Processes
14.4 Epidermal Growth Factor REceptor Dimerization can Drive Signals
14.5 Defects in Signal-Transduction Pathways can lead to Cancer and Other Diseases

Chapter 15:- Metabolism: Basic Concepts and Themes
15.1 Metabolism is composed of many interconnected reactions
15.2 ATP is the Universal Currency of Free Energy in Biological Systems
15.3 The Oxidation of Carbon Fuels is an important Source of Cellular Energy
15.4 Metabolic Pathways Contain many Recurring Motifs

Chapter 16:- Glycolysis and Gluconeogenesis
16.1 Glycolysis is an energy Conversion Pathway in Most Organisms
16.2 Glycolysis can be Divided into Two Parts
16.3 The Glycolytic Pathway is Tightly Controlled
16.4 Glucose Can be Synthesized from Non-carbohydrate Precursors
16.5 Gluconeogenesis and Glycolysis are Reciprocally Regulated

Chapter 17:- Pyruvate Dehydrogenase and the Citric Acid Cycle
17.1 The Citric Acid Cycle Harvests High Energy Electrons
17.2 The Pyruvate Dehydrogenase Complex Links Glycolysis to the Citric Acid Cycle
17.3 The Citric Acid Cycle Oxidizes Two Carbon Units
17.4 Entry to the Citric Acid Cycle and Metabolism Through It are Controlled
17.5 The Citric Acid Cycle is a Source of Biosynthetic Precursors

Chapter 18:- Oxidative Phosphorylation
18.1 Cellular Respiration Drives ATP Formation by Transferring Electrons to Molecular Oxygen
18.2 Oxidative Phosphorylation depends on Electron Transfer
18.3 The Respiratory Chain Consists of Four Complexes
18.4 A Proton Gradients Powers the syntheses of ATP
18.5 Manu Shuttles Allow Movement Across Mitochondrial Membranes

Chapter 19:- Phototrophy and the Light Reactions of Photosynthesis
19.1 Phototrophy converts Light Energy into Chemical Energy
19.2 In Eukaryotes, Photosynthesis Takes Place in Chloroplasts
19.3 Light Obsorption by Chlorophyll Molecules Induces Electron Transfer
19.4 Two Photosystems Generate a Proton Gradient
19.5 A Proton Gradient Across the Thylakoid Membrane Drives ATP Synthesis

Chapter 20:- The Calvin - Benson Cycle and the Pentose Phosphate Pathway
20.1 The Calvin-Benson Cycle Synthesizes Hexoses from Carbon Dioxide and Water
20.2 The Activity of the Calvin-Benson Cycle Depends on Environmental Conditions
20.3 The Pentose Phosphate Pathway Generates NADPH and Synthesizes Pentoses
20.4 The Metabolism of Glucose 6-Phosphate by the Pentose Phosphate Pathway is coordinated with Glyclysis
20.5 Glucose Phosphate Dehydrogenase Plays a Key role in Protection against Reactive Oxygen Species

Chapter 21:- Glycogen Metabolism
21.1 Glycogen Metabolism is the Regulated Release and Storage of Glucose in Multiple Tissues
21.2 Glycogen Breakdown requires the Interplay of Several Enzymes
21.3 Phosphorylase is Regulated by Allosteric Interactions and Controlled by Reversible Phosphorylation
21.4 Glucagon and Epinephrine Signal the need for Glycogen Breakdown
21.5 Glycogen Synthesis Requires Several Enzymes and Uridine Diphosphate Glucose

Chapter 22:- Fatty Acid and Triacylglycerol Metabolism
Chapter 23:- Protein Turnover and Amino Acid Catabolism
Chapter 24:- Integration of Energy Metabolism
Chapter 25:- Biosynthesis of Amino Acid
Chapter 26:- Nucleotide Biosynthesis
Chapter 27:- Biosynthesis of Membrane Lipids and Steroids
Chapter 28:- DNA Replication, Repair, and Recombination
Chapter 29:- RNA Functions, Biosynthesis and Processing
Chapter 30:- Protein Biosynthesis
Chapter 31:- Control of Gene Expression
Chapter 32:- Principles of Drug Discovery and Development

Chemistry Review Appendix
Answers to Self Check Questions
Answers to Problems
Index