Biochemistry / Mary K. Campbell, Shawn O. Farrell

Contents;

1 Biochemistry and the
Organization of Cells
1.1 Basic Themes
1.2 Chemical Foundations of Biochemistry
1.3 The Beginnings of Biology: Origin of Life 5 The Earth and Its Age
Biochemical Connections: Why Structural Formulas Are So Important
Biomolecules
Molecules to Cells
1.4 The Biggest Biological Distinction—Prokaryotes and Eukaryotes
1.5 Prokaryotic Cells
1.6 Eukaryotic Cells
1.7 Five Kingdoms, Three Domains
Biochemical Connections: Extremophiles: The Toast of the Industry
1.8 Common Ground for All Cells
1.9 Biochemical Energetics
1.10 Energy and Change
1.11 Spontaneity in Biochemical Reactions
1.12 Life and Thermodynamics
Biochemical Connections: Predicting Reactions
Summary
Review Exercises
Annotated Bibliography



2 Water: The Solvent for Biochemical Reactions
2.1 Water and Polarity
Solvent Properties of Water
2.2 Hydrogen Bonds
Other Biologically Important Hydrogen Bonds
Biochemical Connections: How Basic Chemistry Affects Life: The Importance of the Hydrogen Bond
2.3 Acids, Bases, and pH
2.4 Titration Curves
2.5 Buffers
Biochemical Connections: Buffer Selection
Biochemical Connections: Some Physiological Consequences of Blood Buffering
Biochemical Connections: Lactic Acid—Not Always the Bad Guy
Summary
Review Exercises
Annotated Bibliography



3 Amino Acids and Peptides
3.1 Amino Acids Exist in a Three-Dimensional World
3.2 Individual Amino Acids: Their Structures and Properties 66 Uncommon Amino Acids
Biochemical Connections: Amino Acids to Calm Down and Pep Up
3.3 Amino Acids Can Act as Both Acids and Bases
3.4 The Peptide Bond
3.5 Small Peptides with Physiological Activity
Biochemical Connections: Amino Acids Go Many Different Places
Biochemical Connections: Aspartame, the Sweet Peptide
Biochemical Connections: Phenylketonuria—Little Molecules Have Big Effects
Biochemical Connections: Peptide Hormones—More Small Molecules with Big Effects
Summary
Review Exercises
Annotated Bibliography



4 The Three-Dimensional Structure of Proteins
4.1 Protein Structure and Function
4.2 Primary Structure of Proteins
4.3 Secondary Structure of Proteins
Periodic Structures in Protein Backbones
Biochemical Connections: Complete Proteins and Nutrition 90 Irregularities in Regular Structures
Supersecondary Structures and Domains
The Collagen Triple Helix
Two Types of Protein Conformations: Fibrous and Globular
4.4 Tertiary Structure of Proteins
Forces Involved in Tertiary Structures
Myoglobin: An Example of Protein Structure
Denaturation and Refolding
4.5 Quaternary Structure of Proteins 106 Hemoglobin
Conformational Changes That Accompany Hemoglobin Function
4.6 Protein Folding Dynamics
Hydrophobic Interactions: A Case Study in Thermodynamics
The Importance of Correct Folding
Protein-Folding Chaperones
Biochemical Connections: Prions and Disease
Summary
Review Exercises
Annotated Bibliography


5 Protein Purification and Characterization Techniques
5.1 Extracting Pure Proteins from Cells
5.2 Column Chromatography
5.3 Electrophoresis
5.4 Determining the Primary Structure of a Protein
Cleavage of the Protein into Peptides
Sequencing of Peptides: The Edman Method
Biochemical Connections: Pulling It All Together
Summary
Review Exercises
Annotated Bibliography


6 The Behavior of Proteins: Enzymes
6.1 Enzymes Are Effective Biological Catalysts
6.2 Kinetics versus Thermodynamics
Biochemical Connections: Enzymes as Markers for Disease
6.3 Enzyme Kinetic Equations
6.4 Enzyme–Substrate Binding
6.5 Examples of Enzyme-Catalyzed Reactions
6.6 The Michaelis–Menten Approach to Enzyme Kinetics
6.7 Enzyme Inhibition
Biochemical Connections: Practical Information from Kinetic Data
Biochemical Connections: Enzyme Inhibition in the Treatment of AIDS
Summary
Review Exercises
Annotated Bibliography


7 The Behavior of Proteins: Enzymes, Mechanisms, and Control
7.1 The Behavior of Allosteric Enzymes
7.2 The Concerted and Sequential Models for Allosteric Enzymes
7.3 Control of Enzyme Activity by Phosphorylation
7.4 Zymogens
7.5 The Nature of the Active Site
7.6 Chemical Reactions Involved in Enzyme Mechanisms
Biochemical Connections: Enzymes Catalyze Familiar Reactions of Organic Chemistry
7.7 The Active Site and Transition States 1
Biochemical Connections: Families of Enzymes: Proteases
7.8 Coenzymes
Biochemical Connections: Catalytic Antibodies against Cocaine 196 Biochemical Connections: Catalysts for Green Chemistry
Summary
Review Exercises
Annotated Bibliography


8 Lipids and Proteins Are Associated in Biological Membranes
8.1 The Definition of a Lipid
8.2 The Chemical Natures of the Lipid Types
Biochemical Connections: Lipids Have Everything to Do with Multiple Sclerosis
8.3 Biological Membranes
Biochemical Connections: Butter versus Margarine—Which Is Healthier?
8.4 The Kinds of Membrane Proteins
8.5 The Fluid-Mosaic Model of Membrane Structure
Biochemical Connections: Membranes in Drug Delivery
8.6 The Functions of Membranes
Biochemical Connections: Lipid Droplets Are Not Just Great Balls of Fat
8.7 Lipid-Soluble Vitamins and Their Functions
Vitamin A
Vitamin D
Biochemical Connections: Vision Has Great Chemistry
Vitamin E
Vitamin K
8.8 Prostaglandins and Leukotrienes
Biochemical Connections: Why Should We Eat More Salmon?
Summary
Review Exercises
Annotated Bibliography


9 Nucleic Acids: How Structure Conveys Information
9.1 Levels of Structure in Nucleic Acids
9.2 The Covalent Structure of Polynucleotides
Biochemical Connections: The DNA Family Tree
9.3 The Structure of DNA
Biochemical Connections: What Makes a Triple Helix Useful in Drug Design?
9.4 Denaturation of DNA
9.5 The Principal Kinds of RNA and Their Structures
Biochemical Connections: The Human Genome Project: Treasure or Pandora’s Box?
Biochemical Connections: Why Identical Twins Are Not Identical
Summary
Review Exercises
Annotated Bibliography


10 Biosynthesis of Nucleic Acids: Replication
10.1 The Flow of Genetic Information in the Cell
10.2 Replication of DNA
Semiconservative Replication
10.3 DNA Polymerase
Semidiscontinuous DNA Replication 265 DNA Polymerase from E. coli
10.4 Proteins Required for DNA Replication
Supercoiling and Replication
The Primase Reaction
Synthesis and Linking of New DNA Strands
10.5 Proofreading and Repair
Biochemical Connections: Why Does DNA Contain Thymine and Not Uracil? 276
10.6 Eukaryotic DNA Replication
Biochemical Connections: The SOS Response in E. coli
Eukaryotic DNA Polymerases
Biochemical Connections: Telomerase and Cancer 282 The Eukaryotic Replication Fork
Summary
Review Exercises
Annotated Bibliography


11 Transcription of the Genetic Code: The Biosynthesis of RNA
11.1 Overview of Transcription
11.2 Transcription in Prokaryotes 288 RNA Polymerase in Escherichia coli
Promoter Structure
Chain Initiation
Chain Elongation
Chain Termination
11.3 Transcription Regulation in Prokaryotes Alternative σ Factors
Enhancers
Operons
Transcription Attenuation
11.4 Transcription in Eukaryotes
Structure of RNA Polymerase II
Pol II Promoters
Initiation of Transcription
Elongation and Termination
11.5 Transcription Regulation in Eukaryotes
11.6 Enhancers and Silencers
Biochemical Connections: TFIIH—Making the Most Out of the Genome
Response Elements
RNA Interference
11.7 Structural Motifs in DNA-Binding Proteins
Biochemical Connections: CREB—The Most Important Protein You
Have Never Heard Of?
DNA-Binding Domains
Helix–Turn–Helix Motifs
Zinc Fingers
Basic-Region Leucine Zipper Motif 317 Transcription-Activation Domains
11.8 Posttranscriptional RNA Modification
11.9 Transfer RNA and Ribosomal RNA
Messenger RNA
The Splicing Reaction: Lariats and Snurps
Alternative RNA Splicing
Biochemical Connections: Lupus: An Autoimmune Disease Involving RNA Processing
11.10 Ribozymes
Biochemical Connections: Proofreading in Transcription? RNA Fills In Another Missing Piece
Summary
Review Exercises
Annotated Bibliography


12 Protein Synthesis: Translation of the Genetic Message
12.1 Translating the Genetic Message
12.2 The Genetic Code
Codon–Anticodon Pairing and Wobble
12.3 Amino Acid Activation
12.4 Prokaryotic Translation
Ribosomal Architecture
Chain Initiation
Chain Elongation
Chain Termination
The Ribosome Is a Ribozyme
Biochemical Connections: The 21st Amino Acid?
Polysomes
12.5 Eukaryotic Translation
Chain Initiation
Chain Elongation
Chain Termination
Coupled Transcription and Translation in Eukaryotes?
12.6 Posttranslational Modification of Proteins
12.7 Protein Degradation
Biochemical Connections: Chaperones: Preventing Unsuitable Associations
Biochemical Connections: Silent Mutations Are Not Always Silent
Biochemical Connections: How Do We Adapt to High Altitude?
Summary
Review Exercises
Annotated Bibliography


13 Nucleic Acid Biotechnology Techniques
13.1 Purification and Detection of Nucleic Acids
Separation Techniques
Detection Methods
13.2 Restriction Endonucleases
Many Restriction Endonucleases Produce
“Sticky Ends”
13.3 Cloning
Using “Sticky Ends” to Construct Recombinant DNA
13.4 Genetic Engineering 375 DNA Recombination Occurs in Nature
Bacteria as “Protein Factories”
Biochemical Connections: Genetic Engineering in Agriculture
Protein Expression Vectors
Genetic Engineering in Eukaryotes
Biochemical Connections: Human Proteins through Genetic Recombination Techniques 381
13.5 DNA Libraries
Biochemical Connections: Fusion Proteins and Fast Purifications 383 Finding an Individual Clone in a DNA Library
13.6 The Polymerase Chain Reaction
13.7 DNA Fingerprinting
Biochemical Connections: CSI: Biochemistry—Forensic Uses of DNA Testing
Restriction-Fragment Length Polymorphisms:
A Powerful Method for Forensic Analysis
13.8 Sequencing DNA
Biochemical Connections: RNA Interference—The Newest Way to Study Genes
13.9 Genomics and Proteomics
The Power of Microarrays—Robotic Technology Meets Biochemistry
Protein Arrays
Summary
Review Exercises
Annotated Bibliography



14 Viruses, Cancer, and Immunology
14.1 Viruses
Families of Viruses
Virus Life Cycles
14.2 Retroviruses
Biochemical Connections: Viruses Are Used for Gene Therapy
14.3 The Immune System
Innate Immunity—The Front Lines of Defense
Acquired Immunity: Cellular Aspects
T-Cell Functions
T-Cell Memory
The Immune System: Molecular Aspects
Distinguishing Self from Nonself
Biochemical Connections: Viral RNAs Outwit the Immune System
14.4 Cancer 425 Oncogenes Tumor Suppressors
14.5 Viruses and Cancer
Viruses Helping Cure Cancer
Biochemical Connections: Attacking the Symptoms instead of the Disease?
Summary
Review Exercises
Annotated Bibliography


15 The Importance of Energy Changes and Electron Transfer in Metabolism
15.1 Standard States for Free-Energy Changes
15.2 A Modified Standard State for Biochemical
Applications
Biochemical Connections: Living Things Need Energy—How Do They Use It?
15.3 The Nature of Metabolism
Biochemical Connections: Living Things Are Unique Thermodynamic Systems
15.4 The Role of Oxidation and Reduction in Metabolism
15.5 Coenzymes in Biologically Important Oxidation–Reduction Reactions
15.6 Coupling of Production and Use of Energy
15.7 Coenzyme A in Activation of Metabolic Pathways
Summary
Review Exercises
Annotated Bibliography


16 Carbohydrates
16.1 Sugars: Their Structures and Stereochemistry
16.2 Reactions of Monosaccharides
Biochemical Connections: Vitamin C Is Related to Sugars
16.3 Some Important Oligosaccharides
Biochemical Connections: Fruits, Flowers, Striking Colors, and Medicinal Uses Too
Biochemical Connections: Lactose Intolerance: Why Do So Many People Not Want to Drink Milk?
16.4 Structures and Functions of Polysaccharides
Biochemical Connections: Why Is Dietary Fiber So Good for You?
16.5 Glycoproteins 486
Biochemical Connections: Low-Carbohydrate Diets
Biochemical Connections: Glycoproteins and Blood Transfusions
Summary
Review Exercises
Annotated Bibliography


17 Glycolysis
17.1 The Overall Pathway of Glycolysis
Biochemical Connections: Biofuels from Fermentation
17.2 Conversion of Six-Carbon Glucose to Three-Carbon Glyceraldehyde-3-Phosphate
17.3 Glyceraldehyde-3-Phosphate Is Converted to Pyruvate
17.4 Anaerobic Metabolism of Pyruvate
Biochemical Connections: What Is the Connection between Anaerobic Metabolism and Dental Plaque?
Biochemical Connections: Fetal Alcohol Syndrome
17.5 Energy Production in Glycolysis
Summary
Review Exercises
Annotated Bibliography

18 Storage Mechanisms and Control in Carbohydrate Metabolism
18.1 How Glycogen Is Produced and Degraded
Biochemical Connections: Why Do Athletes Go In for Glycogen Loading?
18.2 Gluconeogenesis Produces Glucose from Pyruvate
18.3 Control of Carbohydrate Metabolism
18.4 Glucose Is Sometimes Diverted through the Pentose Phosphate Pathway
Biochemical Connections: The Pentose Phosphate Pathway and Hemolytic Anemia
Summary
Review Exercises
Annotated Bibliography


19 The Citric Acid Cycle 545
19.1 The Central Role of the Citric Acid Cycle in Metabolism
19.2 The Overall Pathway of the Citric Acid Cycle
19.3 How Pyruvate Is Converted to Acetyl-CoA
19.4 The Individual Reactions of the Citric Acid Cycle
Biochemical Connections: Plant Poisons and the Citric Acid Cycle
19.5 Energetics and Control of the Citric Acid Cycle
19.6 The Glyoxylate Cycle: A Related Pathway
19.7 The Citric Acid Cycle in Catabolism
19.8 The Citric Acid Cycle in Anabolism
Biochemical Connections: Why Can’t Animals Use All the Same Energy Sources as Plants and Bacteria?
19.9 The Link to Oxygen
Summary
Biochemical Connections: Why Is It So Hard to Lose Weight?
Summary
Review Exercises
Annotated Bibliography


20 Electron Transport and Oxidative Phosphorylation
20.1 The Role of Electron Transport in Metabolism
20.2 Reduction Potentials in the Electron Transport Chain
20.3 Organization of Electron Transport Complexes
20.4 The Connection between Electron Transport and Phosphorylation
20.5 The Mechanism of Coupling in Oxidative Phosphorylation
20.6 Respiratory Inhibitors Can Be Used to Study Electron Transport
20.7 Shuttle Mechanisms
Biochemical Connections: What Does Brown Adipose Tissue Have to Do with Obesity?
20.8 The ATP Yield from Complete Oxidation of Glucose
Biochemical Connections: Sports and Metabolism
Summary
Biochemical Connections: The Darker Side of Sports
Summary
Review Exercises
Annotated Bibliography



21 Lipid Metabolism
21.1 Lipids Are Involved in the Generation and Storage of Energy
21.2 Catabolism of Lipids
21.3 The Energy Yield from the Oxidation of Fatty Acids
21.4 Catabolism of Unsaturated Fatty Acids and Odd-Carbon Fatty Acids
21.5 Ketone Bodies
21.6 Fatty-Acid Biosynthesis
Biochemical Connections: Ketone Bodies and Effective Weight Loss
21.7 Synthesis of Acylglycerols and Compound Lipids
Biochemical Connections: A Gene for Obesity
Triacylglycerols
Biochemical Connections: Acetyl-CoA Carboxylase—A New Target in the Fight against Obesity?
21.8 Cholesterol Biosynthesis
Biochemical Connections: Atherosclerosis
Summary
Review Exercises
Annotated Bibliography



22 Photosynthesis
22.1 Chloroplasts Are the Site of Photosynthesis
Biochemical Connections: The Relationship between Wavelength and Energy of Light
22.2 Photosystems I and II and the Light Reactions of Photosynthesis
Cyclic Electron Transport in Photosystem
22.3 Photosynthesis and ATP Production
Biochemical Connections: Killing Weeds by Inhibiting
Photosynthesis
22.4 Evolutionary Implications of Photosynthesis with and without Oxygen
22.5 Dark Reactions of Photosynthesis Fix CO2
22.6 CO2 Fixation in Tropical Plants
Biochemical Connections: Chloroplast Genes
Summary
Review Exercises
Annotated Bibliography


23 The Metabolism of Nitrogen
23.1 Nitrogen Metabolism: An Overview
23.2 Nitrogen Fixation
Biochemical Connections: Why Is the Nitrogen Content of Fertilizers So Important?
23.3 Feedback Inhibition in Nitrogen Metabolism
23.4 Amino Acid Biosynthesis
23.5 Essential Amino Acids
23.6 Amino Acid Catabolism
Excretion of Excess Nitrogen
Biochemical Connections: Water and the Disposal of Nitrogen Wastes
Biochemical Connections: Chemotherapy and Antibiotics—Taking Advantage of the Need for Folic Acid
23.7 Purine Biosynthesis
Anabolism of Inosine Monophosphate
23.8 Purine Catabolism
Biochemical Connections: Lesch–Nyhan Syndrome
23.9 Pyrimidine Biosynthesis and Catabolism
23.10 The Anabolism of Pyrimidine Nucleotides Pyrimidine Catabolism
23.11 Conversion of Ribonucleotides to Deoxyribonucleotides
23.12 Conversion of dUTP to dTTP
Summary
Review Exercises
Annotated Bibliography


24 Integration of Metabolism: Cellular Signaling
24.1 Connections between Metabolic Pathways
24.2 Biochemistry and Nutrition
Biochemical Connections: Alcohol Consumption and Addiction
Biochemical Connections: Iron: An Example of a Mineral Requirement
The Food Pyramid
24.3 Hormones and Second Messengers
Hormones
Second Messengers
Cyclic AMP and G Proteins
Calcium Ion as a Second Messenger
Receptor Tyrosine Kinases
24.4 Hormones and the Control of Metabolism
24.5 Insulin and Its Effects 728 Insulin Receptors
Insulin’s Effect on Glucose Uptake
Biochemical Connections: Insulin and Low-Carbohydrate Diets
Insulin Affects Many Enzymes
Diabetes
Insulin and Sports
Biochemical Connections: A Workout a Day Keeps Diabetes Away?
Biochemical Connections: The Search for Longevity
Summary
Review Exercises
Annotated Bibliography

Includes bibliographic references and index.