Biochemistry Extended, Chapters 1-34 / Edition 5

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Overview

This book is an outgrowth of my teaching of biochemistry to undergraduates, graduate students, and medical students at Yale and Stanford. My aim is to provide an introduction to the principles of biochemistry that gives the reader a command of its concepts and language. I also seek to give an appreciation of the process of discovery in biochemistry.

This book provides a comprehensive introduction to the principles of biochemistry, giving the reader a command of biochemistry's basic concepts of language.

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Product Details

  • ISBN-13: 9780716730514
  • Publisher: Freeman, W. H. & Company
  • Publication date: 2/28/2002
  • Edition description: Fifth Edition
  • Edition number: 5
  • Pages: 1050
  • Product dimensions: 8.75 (w) x 11.12 (h) x 1.40 (d)

Read an Excerpt

Space, time, and energy are discussed from a biochemical perspective. (pages 5-6)

1. Space:
To help yourself visualize relative scale, note the size of a molecule you are studying and compare it with others. For example, glucose, one of the most commonly discussed carbohydrate molecules in metabolism, has a length of about 8 angstroms. Compare it with the blood protein molecule hemoglobin, about 65 angstroms across at its widest diameter.

Stryer uses the angstrom (Å) as a unit of dimension for structures less than 100 angstroms in size, and the units nm (nanometer) or mm (micrometer) for longer dimensions.

2. Time:
Times required for reactions at the atomic or even the molecular level are extremely short, ranging from a few picoseconds (10-12 s) to milliseconds (10-3 s) for many enzymatic reactions. The set of biochemical reactions required for the duplication of a bacterial cell takes much longer¾from 15 to 20 minutes, under optimum nutritional conditions¾but nevertheless is rapid compared with many other everyday phenomena.

3. Energy:
Energy changes in biochemical systems range from less than one kilocalorie per mole (kcal/mol), for thermal motion, to several hundred kcal/mol, for the complete oxidation of glucose.

Biochemical reactions that involve the formation or breakage of strong, covalent bonds typically require an energy input as high as 80 kcal/mol.

Three types of weak attractive forces are essential to biological structures and processes. (pages 7-9)

4. Electrostatic bonds:
(such as ionic interactions), or salt bridges. Note on page 7 how the strength of these bonds is strongly dependent on the dielectric constant of the medium. (Energies range from 3 to 7 kcal/mol.) Bonding between two oppositely charged ions in a protein is stronger if the pair is buried in the interior of the molecule, from which water is excluded.

5. Hydrogen bonds: These bonds can involve either uncharged or charged molecules. The sharing of a hydrogen atom by two other atoms is strongest when the three atoms lie in a straight line. (Energies range from 3 to 7 kcal/mol.)

Stryer cites the a helix of proteins and DNA base pairing as good examples of hydrogen bonding. Other examples are interactions among proteins and nucleotides, as occurs in transcription and translation, and interactions between macromolecules and water (or other small polar molecules).

6. Van der Waals interactions:
These are the weakest of the three types of noncovalent forces. Van der Waals attractions between adjacent atoms are due to temporary asymmetries in the distribution of their electrons, and to steric complementarities within a group of atoms. (Energy of about 1 kcal/mol.)

Water is intimately involved in all aspects of biochemistry and molecular biology. (pages 9-10)

7. Properties of water:
Stryer also summarizes the unique properties that make water biologically important. Water molecules are polar and hence are readily able to form hydrogen bonds among themselves. The same properties also allow water to compete for ionic and hydrogen bonds between polar molecules, making it an excellent solvent for polar substances.

Nonaqueous environments are also important in biochemical structure and function. (page 11)

8. Hydrophobic interactions:
Chapter 1 closes with a discussion of hydrophobic interactions among biological molecules. Nonpolar groups surrounded by water associate with each other, not only because they have an affinity for each other, but primarily because water molecules have a greater tendency to form hydrogen bonds with each other than with nonpolar molecules. This phenomenon is important in the formation of membrane lipid bilayers. It also plays a role in the folding of protein chains to form globular structures whose interiors are virtually free of water (see figure 2-44).

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Table of Contents

Preface
Ch. 1 Prelude: Biochemistry and the Genomic Revolution
Ch. 2 Biochemical Evolution
Ch. 3 Protein Structure and Function
Ch. 4 Exploring Proteins
Ch. 5 DNA, RNA, and the Flow of Genetic Information
Ch. 6 Exploring Genes
Ch. 7 Exploring Evolution (Including Bioinformatics)
Ch. 8 Enzymes: Basic Concepts and Kinetics
Ch. 9 Catalytic Strategies
Ch. 10 Regulatory Strategies: Enzymes and Hemoglobin
Ch. 11 Carbohydrates
Ch. 12 Lipids and Cell Membranes
Ch. 13 Membrane Channels and Pumps
Ch. 14 Metabolism: Basic Concepts and Design
Ch. 15 Signal-Transduction Pathways: An Introduction to Information Metabolism
Ch. 16 Glycolysis and Gluconeogenesis
Ch. 17 The Citric Acid Cycle
Ch. 18 Oxidative Phosphorylation
Ch. 19 The Light Reactions of Photosynthesis
Ch. 20 The Calvin Cycle and the Pentose Phosphate Pathway
Ch. 21 Glycogen Metabolism
Ch. 22 Fatty Acid Metabolism
Ch. 23 Protein Turnover and Amino Acid Catabolism
Ch. 24 The Biosynthesis of Amino Acids
Ch. 25 Nucleotide Biosynthesis
Ch. 26 The Biosynthesis of Membrane Lipids and Steroids
Ch. 27 DNA Replication, Recombination, and Repair
Ch. 28 RNA Synthesis and Splicing
Ch. 29 Protein Synthesis
Ch. 30 The Integration of Metabolism
Ch. 31 The Control of Gene Expression
Ch. 32 Sensory Systems
Ch. 33 The Immune System
Ch. 34 Molecular Motors
Appendixes
Glossary of Compounds
Answers to Problems
Index
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