Essential Biochemistry, International Adaptation

CHARLOTTE PRATT received a B.S. in biology from the University of Notre Dame and a Ph.D. in biochemistry from Duke University. She is a protein chemist who has conducted research in blood coagulation and inflammation at the University of North Carolina at Chapel Hill. She is currently Associate Professor in the Biology Department at Seattle Pacific University. Her interests include molecular evolution, enzyme action, and the relationship between metabolic processes and disease. She has written numerous research and review articles, has worked as a textbook editor, and is a co-author, with Donald Voet and Judith G. Voet, of Fundamentals of Biochemistry, published by John Wiley & Sons, Inc. KATHLEEN CORNELY holds a B.S. in chemistry from Bowling Green (Ohio) State University, an M.S. in biochemistry from Indiana University, and a Ph.D. in nutritional biochemistry from Cornell University. She is currently the Robert H. Walsh '39 Endowed Professor in Chemistry and Biochemistry at Providence College, where she has focused on expanding the use of case studies and guided inquiry across a broad spectrum of classes. Her interest in active pedagogy has led to her involvement in national programs including Project Kaleidoscope, the POGIL Project, and the Howard Hughes Medical Institute SEA PHAGES program, which has also fueled her current experimental research in phage genomics. She has been a member of the editorial board of Biochemistry and Molecular Biology Education and has served for several years as coordinator of the undergraduate poster competition at the annual meeting of the American Society for Biochemistry and Molecular Biology.

Part 1 FOUNDATIONS

1 The Chemical Basis of Life

1.1 What Is Biochemistry?

1.2 The Origin of Cells

1.3 Biological Molecules

1.4 Energy and Metabolism

 

2 Aqueous Chemistry

2.1 Water Molecules and Hydrogen Bonds

2.2 The Hydrophobic Effect

2.3 Acid–Base Chemistry

2.4 Tools and Techniques: Buffers

2.5 Clinical Connection: Physiological Buffers

 

Part 2 MOLECULAR STRUCTURE AND FUNCTION

3 Nucleic Acid Structure and Function

3.1 Nitrogenous Bases

3.2 Nucleic Acid Structure

3.3 The Central Dogma

3.4 Genomics

 

4 Amino Acid and Protein Structure

4.1 Amino Acids, the Building Blocks of Proteins

4.2 Secondary Structure: The Conformation of the Peptide Group

4.3 Tertiary Structure and Protein Stability

4.4 Quaternary Structure

4.5 Clinical Connection: Protein Misfolding and Disease

4.6 Tools and Techniques: Analyzing Protein Structure

 

5 Protein Function

5.1 Myoglobin and Hemoglobin: Oxygen-Binding Proteins

5.2 Clinical Connection: Hemoglobin Variants

5.3 Structural Proteins

5.4 Motor Proteins

5.5 Antibodies

 

6 Enzymes: Classification and Catalysis

6.1 What Is an Enzyme?

6.2 Chemical Catalytic Mechanisms

6.3 Unique Properties of Enzyme Catalysts

6.4 Chymotrypsin in Context

6.5 Clinical Connection: Blood Coagulation

 

7 Enzyme Kinetics and Inhibition

7.1 Introduction to Enzyme Kinetics

7.2 The Michaelis–Menten Equation for an Enzyme-Catalyzed Reaction

7.3 Enzyme Inhibition

7.4 Clinical Connection: Drug Development

 

8 Lipids and Biological Membranes

8.1 Lipids

8.2 The Lipid Bilayer

8.3 Membrane Proteins

8.4 The Fluid Mosaic Model

 

9 Membrane Transport

9.1 The Thermodynamics of Membrane Transport

9.2 Passive Transport

9.3 Active Transport

9.4 Membrane Fusion



10 Signaling

10.1 General Features of Signaling Pathways

10.2 G Protein Signaling Pathways

10.3 Receptor Tyrosine Kinases

10.4 Lipid Hormone Signaling

 

11 Carbohydrates

11.1 Monosaccharides

11.2 Disaccharides, Oligosaccharides, and Polysaccharides

11.3 Glycoconjugates: Glycoproteins, Glycolipids, and Proteoglycans

11.4 Clinical Connection: Glucose and Diabetes Mellitus

 

Part 3 METABOLISM

12 Metabolism and Bioenergetics

12.1 Food and Fuel

12.2 Free Energy Changes in Metabolic Reactions

12.3 Metabolic Pathways

 

13 Carbohydrate Metabolism

13.1 Glycolysis 

13.2 Gluconeogenesis

13.3 Glycogen Synthesis and Degradation

13.4 The Pentose Phosphate Pathway

13.5 Clinical Connection: Disorders of Carbohydrate Metabolism

 

14 The Citric Acid Cycle

14.1 The Pyruvate Dehydrogenase Reaction

14.2 The Eight Reactions of the Citric Acid Cycle

14.3 Thermodynamics of the Citric Acid Cycle

14.4 Anabolic and Catabolic Functions of the Citric Acid Cycle

 

15 Oxidative Phosphorylation

15.1 The Thermodynamics of Oxidation-Reduction Reactions

15.2 Mitochondrial Electron Transport

15.3 ATP Synthase

15.4 Chemiosmosis

 

16 Photosynthesis

16.1 Photosynthesis: An Overview

16.2 The Light Reactions

16.3 Carbon Fixation

 

17 Lipid Metabolism

17.1 Lipid Digestion and Transport

17.2 Fatty Acid Oxidation

17.3 Fatty Acid Synthesis

17.4 Synthesis of Other Lipids

 

18 Nitrogen Metabolism

18.1 Nitrogen Fixation and Assimilation

18.2 Amino Acid Biosynthesis

18.3 Amino Acid Catabolism

18.4 Excretion of Excess Nitrogen: The Urea Cycle

18.5 Nucleotide Metabolism

 

19 Regulation of Mammalian Fuel Metabolism

19.1 Integration of Fuel Metabolism

19.2 Hormonal Control of Fuel Metabolism

19.3 Disorders of Fuel Metabolism

19.4 Clinical Connection: Cancer Metabolism

 

Part 4 GENETIC INFORMATION

20 DNA Replication and Repair

20.1 DNA Packaging: Nucleosome and Chromatin

20.2 The DNA Replication Machinery

20.3 Telomeres

20.4 DNA Damage and Repair

20.5 Clinical Connection: Cancer as a Genetic Disease

20.6 Tools and Techniques: Manipulating DNA

 

 

21 Transcription and RNA Processing

21.1 Initiating Transcription

21.2 RNA Polymerase

21.3 RNA Processing

 

22 Protein Synthesis

22.1 tRNA and the Genetic Code

22.2 Ribosome Structure

22.3 Translation

22.4 Post-Translational Modifications

 

GLOSSARY

ODD-NUMBERED SOLUTIONS

INDEX