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Table of Contents
                            Table of Contents
Dedication
About the authors
Preface
	Tools and Techniques
	Clinical Applications
	Molecular Evolution
	Supplements Supporting Biochemistry, Fifth Edition
Acknowledgments
I. The Molecular Design of Life
	1. Prelude: Biochemistry and the Genomic Revolution
		1.1. DNA Illustrates the Relation between Form and Function
		1.2. Biochemical Unity Underlies Biological Diversity
		1.3. Chemical Bonds in Biochemistry
		1.4. Biochemistry and Human Biology
		Appendix: Depicting Molecular Structures
                        
Document Text Contents
Page 1

Dedication

About the authors

Preface
Tools and Techniques
Clinical Applications
Molecular Evolution
Supplements Supporting Biochemistry, Fifth Edition

Acknowledgments

I. The Molecular Design of Life
1. Prelude: Biochemistry and the Genomic Revolution

1.1. DNA Illustrates the Relation between Form and Function
1.2. Biochemical Unity Underlies Biological Diversity
1.3. Chemical Bonds in Biochemistry
1.4. Biochemistry and Human Biology
Appendix: Depicting Molecular Structures

2. Biochemical Evolution
2.1. Key Organic Molecules Are Used by Living Systems
2.2. Evolution Requires Reproduction, Variation, and Selective Pressure
2.3. Energy Transformations Are Necessary to Sustain Living Systems
2.4. Cells Can Respond to Changes in Their Environments
Summary
Problems
Selected Readings

3. Protein Structure and Function
3.1. Proteins Are Built from a Repertoire of 20 Amino Acids
3.2. Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide
Chains
3.3. Secondary Structure: Polypeptide Chains Can Fold Into Regular Structures Such as the
Alpha Helix, the Beta Sheet, and Turns and Loops
3.4. Tertiary Structure: Water-Soluble Proteins Fold Into Compact Structures with Nonpolar
Cores
3.5. Quaternary Structure: Polypeptide Chains Can Assemble Into Multisubunit Structures
3.6. The Amino Acid Sequence of a Protein Determines Its Three-Dimensional Structure
Summary
Appendix: Acid-Base Concepts
Problems
Selected Readings

4. Exploring Proteins
4.1. The Purification of Proteins Is an Essential First Step in Understanding Their Function

Page 757

Down syndrome

Retrolental fibroplasia

Cerebrovascular disorders

Ischemia; reperfusion injury

Source: After D.B. Marks, A.D. Marks, and C.M. Smith, Basic Medical Biochemistry: A Clinical Approach (Williams & Wilkins,
1996, p. 331).

II. Transducing and Storing Energy 18. Oxidative Phosphorylation 18.3. The Respiratory Chain Consists of Four Complexes: Three Proton Pumps and a Physical Link to the Citric Acid Cycle



Figure 18.23. Conservation of the Three-Dimensional Structure of Cytochrome C. The side chains are shown for the
21 conserved amino acids and the heme.

II. Transducing and Storing Energy 18. Oxidative Phosphorylation 18.3. The Respiratory Chain Consists of Four Complexes: Three Proton Pumps and a Physical Link to the Citric Acid Cycle



Figure 18.24. Evolutionary Tree Constructed From Sequences of Cytochrome C. Branch lengths are proportional to
the number of amino acid changes that are believed to have occurred. This drawing is an adaptation of the work of
Walter M. Fitch and Emanuel Margoliash.

Page 758

II. Transducing and Storing Energy 18. Oxidative Phosphorylation

18.4. A Proton Gradient Powers the Synthesis of ATP

Conceptual Insights, Energy Transformations in Oxidative
Phosphorylation. View this media module for an animated, interactive
summary of how electron transfer potential is converted into proton-motive
force and, finally, phosphoryl transfer potential in oxidative phosphorylation.

Thus far, we have considered the flow of electrons from NADH to O2, an exergonic process.



Next, we consider how this process is coupled to the synthesis of ATP, an endergonic process.



A molecular assembly in the inner mitochondrial membrane carries out the synthesis of ATP. This enzyme complex was
originally called the mitochon-drial ATPase or F

1
F

0
ATPase because it was discovered through its catalysis of the

reverse reaction, the hydrolysis of ATP. ATP synthase, its preferred name, emphasizes its actual role in the
mitochondrion. It is also called Complex V.

How is the oxidation of NADH coupled to the phosphorylation of ADP? It was first suggested that electron transfer leads
to the formation of a covalent high-energy intermediate that serves as a high phosphoryl transfer potential compound or
to the formation of an activated protein conformation, which then drives ATP synthesis. The search for such
intermediates for several decades proved fruitless.

In 1961, Peter Mitchell proposed that electron transport and ATP synthesis are coupled by a proton gradient across the
inner mitochondrial membrane rather than by a covalent high-energy intermediate or an activated protein conformation.
In his model, the transfer of electrons through the respiratory chain leads to the pumping of protons from the matrix to
the cytosolic side of the inner mitochondrial membrane. The H+ concentration becomes lower in the matrix, and an
electrical field with the matrix side negative is generated (Figure 18.25). Mitchell's idea, called the chemiosmotic
hypothesis, was that this proton-motive force drives the synthesis of ATP by ATP synthase. Mitchell's highly innovative
hypothesis that oxidation and phosphorylation are coupled by a proton gradient is now supported by a wealth of
evidence. Indeed, electron transport does generate a proton gradient across the inner mitochondrial membrane. The pH
outside is 1.4 units lower than inside, and the membrane potential is 0.14 V, the outside being positive. As we calculated
in Section 18.2.2, this membrane potential corresponds to a free energy of 5.2 kcal (21.8 kJ) per mole of protons.

An artificial system was created to elegantly demonstrate the basic principle of the chemiosmotic hypothesis. Synthetic
vesicles containing bacteriorhodopsin, a purple-membrane protein from halobacteria that pumps protons when
illuminated, and mitochondrial ATP synthase purified from beef heart were created (Figure 18.26). When the vesicles
were exposed to light, ATP was formed. This key experiment clearly showed that the respiratory chain and ATP
synthase are biochemically separate systems, linked only by a proton-motive force.

18.4.1. ATP Synthase Is Composed of a Proton-Conducting Unit and a Catalytic Unit

Biochemical, electron microscopic, and crystallographic studies of ATP synthase have revealed many details of its
structure (Figure 18.27). It is a large, complex membrane-embedded enzyme that looks like a ball on a stick. The 85-Å-

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