BioChemistry 6th Edition by Reginald Garrett, Charles Grisham 1305577205 9781305577206

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ISBN 10: 1305577205

ISBN 13: 9781305577206

Author: Reginald H Garrett, Charles M Grisham

Continuing Garrett and Grisham’s innovative conceptual and organizing “Essential Questions” framework, BIOCHEMISTRY guides students through course concepts in a way that reveals the beauty and usefulness of biochemistry in the everyday world. Offering a balanced and streamlined presentation, this edition has been updated throughout with new material and revised presentations.

BioChemistry 6th Table of contents:

Part I. Molecular Components of Cells

Chapter 1. The Facts of Life: Chemistry Is the Logic of Biological Phenomena

1.1. What Are the Distinctive Properties of Living Systems?

1.2. What Kinds of Molecules Are Biomolecules?

1.2a. Biomolecules Are Carbon Compounds

1.3. What Is the Structural Organization of Complex Biomolecules?

1.3a. Metabolites Are Used to Form the Building Blocks of Macromolecules

1.3b. Organelles Represent a Higher Order in Biomolecular Organization

1.3c. Membranes Are Supramolecular Assemblies that Define the Boundaries of Cells

1.3d. The Unit of Life Is the Cell

1.4. How Do the Properties of Biomolecules Reflect Their Fitness to the Living Condition?

1.4a. Biological Macromolecules and Their Building Blocks Have a “Sense” or Directionality

1.4b. Biological Macromolecules Are Informational

1.4c. Biomolecules Have Characteristic Three-Dimensional Architecture

1.4d. Weak Forces Maintain Biological Structure and Determine Biomolecular Interactions

1.4e. Van der Waals Attractive Forces Play an Important Role in Biomolecular Interactions

1.4f. Hydrogen Bonds Are Important in Biomolecular Interactions

1.4g. The Defining Concept of Biochemistry Is “Molecular Recognition through Structural Complementarity”

1.4h. Biomolecular Recognition Is Mediated by Weak Chemical Forces

1.4i. Weak Forces Restrict Organisms to a Narrow Range of Environmental Conditions

1.4j. Enzymes Catalyze Metabolic Reactions

1.4k. The Time Scale of Life

1.5. What Are the Organization and Structure of Cells?

1.5a. The Eukaryotic Cell Likely Emerged from an Archaeal Lineage

1.5b. How Many Genes Does a Cell Need?

1.5c. Archaea and Bacteria Have a Relatively Simple Structural Organization

1.5d. The Structural Organization of Eukaryotic Cells Is More Complex than That of Prokaryotic Cells

1.6. What Are Viruses?

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 2. Water: The Medium of Life

2.1. What Are the Properties of Water?

2.1a. Water Has Unusual Properties

2.1b. Hydrogen Bonding in Water Is Key to Its Properties

2.1c. The Structure of Ice Is Based on H -Bond Formation

2.1d. Molecular Interactions in Liquid Water Are Based on H Bonds

2.1e. The Solvent Properties of Water Derive from Its Polar Nature

2.1f. Water Can Ionize to Form H + and OH –

2.2. What Is pH?

2.2a. Strong Electrolytes Dissociate Completely in Water

2.2b. Weak Electrolytes Are Substances that Dissociate Only Slightly in Water

2.2c. The Henderson–Hasselbalch Equation Describes the Dissociation of a Weak Acid in the Presence of Its Conjugate Base

2.2d. Titration Curves Illustrate the Progressive Dissociation of a Weak Acid

2.2e. Phosphoric Acid Has Three Dissociable H +

2.3. What Are Buffers, and What Do They Do?

2.3a. The Phosphate Buffer System Is a Major Intracellular Buffering System

2.3b. The Imidazole Group of Histidine Also Serves as an Intracellular Buffering System

2.3c. “Good” Buffers Are Buffers Useful within Physiological pH Ranges

2.4. What Properties of Water Give It a Unique Role in the Environment?

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 3. Thermodynamics of Biological Systems

3.1. What Are the Basic Concepts of Thermodynamics?

3.1a. Three Quantities Describe the Energetics of Biochemical Reactions

3.1b. All Reactions and Processes Follow the Laws of Thermodynamics

3.1c. Free Energy Provides a Simple Criterion for Equilibrium

3.2. What Is the Effect of Concentration on Net Free Energy Changes?

3.3. What Is the Effect of pH on Standard-State Free Energies?

3.4. What Can Thermodynamic Parameters Tell Us about Biochemical Events?

3.5. What Are the Characteristics of High-Energy Biomolecules?

3.5a. ATP Is an Intermediate Energy-Shuttle Molecule

3.5b. Group Transfer Potentials Quantify the Reactivity of Functional Groups

3.5c. The Hydrolysis of Phosphoric Acid Anhydrides Is Highly Favorable

3.5d. The Hydrolysis Δ G ° ′ of ATP and ADP Is Greater than That of AMP

3.5e. Acetyl Phosphate and 1,3-Bisphosphoglycerate Are Phosphoric-Carboxylic Anhydrides

3.5f. Enol Phosphates Are Potent Phosphorylating Agents

3.6. What Are the Complex Equilibria Involved in ATP Hydrolysis?

3.6a. The Δ G ° ′ of Hydrolysis for ATP Is pH-Dependent

3.6b. Metal Ions Affect the Free Energy of Hydrolysis of ATP

3.6c. Concentration Affects the Free Energy of Hydrolysis of ATP

3.7. Why Are Coupled Processes Important to Living Things?

3.8. What Is the Daily Human Requirement for ATP?

3.9. What Are Reduction Potentials, and How Are They Used to Account for Free Energy Changes in Redox Reactions?

3.9a. Standard Reduction Potentials Are Measured in Reaction Half-Cells

3.9b. ℰ o ′ Values Can Be Used to Predict the Direction of Redox Reactions

3.9c. ℰ o ′ Values Can Be Used to Analyze Energy Changes in Redox Reactions

3.9d. The Reduction Potential Depends on Concentration

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 4. Amino Acids and the Peptide Bond

4.1. What Are the Structures and Properties of Amino Acids?

4.1a. Typical Amino Acids Contain a Central Tetrahedral Carbon Atom

4.1b. Amino Acids Can Join via Peptide Bonds

4.1c. There Are 20 Common Amino Acids

4.1d. Are There Other Ways to Classify Amino Acids?

4.1e. Amino Acids 21 and 22 —and More?

4.1f. Several Amino Acids Occur Only Rarely in Proteins

4.2. What Are the Acid–Base Properties of Amino Acids?

4.2a. Amino Acids Are Weak Polyprotic Acids

4.2b. Side Chains of Amino Acids Undergo Characteristic Ionizations

4.3. What Reactions Do Amino Acids Undergo?

4.4. What Are the Optical and Stereochemical Properties of Amino Acids?

4.4a. Amino Acids Are Chiral Molecules

4.4b. Chiral Molecules Are Described by the D , L and ( R , S ) Naming Conventions

4.5. What Are the Spectroscopic Properties of Amino Acids?

4.5a. Phenylalanine, Tyrosine, and Tryptophan Absorb Ultraviolet Light

4.5b. Amino Acids Can Be Characterized by Nuclear Magnetic Resonance

4.6. How Are Amino Acid Mixtures Separated and Analyzed?

4.6a. Amino Acids Can Be Separated by Chromatography

4.7. What Is the Fundamental Structural Pattern in Proteins?

4.7a. The Peptide Bond Has Partial Double-Bond Character

4.7b. The Polypeptide Backbone Is Relatively Polar

4.7c. Peptides Can Be Classified According to How Many Amino Acids They Contain

4.7d. Proteins Are Composed of One or More Polypeptide Chains

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 5. Proteins: Their Primary Structure and Biological Functions

5.1. What Architectural Arrangements Characterize Protein Structure?

5.1a. Proteins Fall into Three Basic Classes According to Shape and Solubility

5.1b. Protein Structure Is Described in Terms of Four Levels of Organization

5.1c. Noncovalent Forces Drive Formation of the Higher Orders of Protein Structure

5.1d. A Protein’s Conformation Can Be Described as Its Overall Three-Dimensional Structure

5.2. How Are Proteins Isolated and Purified from Cells?

5.2a. A Number of Protein Separation Methods Exploit Differences in Size and Charge

5.2b. A Typical Protein Purification Scheme Uses a Series of Separation Methods

5.3. How Is the Amino Acid Analysis of Proteins Performed?

5.3a. Acid Hydrolysis Liberates the Amino Acids of a Protein

5.3b. Chromatographic Methods Are Used to Separate the Amino Acids

5.3c. The Amino Acid Compositions of Different Proteins Are Different

5.4. How Is the Primary Structure of a Protein Determined?

5.4a. The Sequence of Amino Acids in a Protein Is Distinctive

5.4b. Sanger Was the First to Determine the Sequence of a Protein

5.4c. Both Chemical and Enzymatic Methodologies Are Used in Protein Sequencing

5.4d. Step 1. Separation of Polypeptide Chains

5.4e. Step 2. Cleavage of Disulfide Bridges

5.4f. Step 3. N- and C-Terminal Analysis

5.4g. Steps 4 and 5. Fragmentation of the Polypeptide Chain

5.4h. Step 6. Reconstruction of the Overall Amino Acid Sequence

5.4i. The Amino Acid Sequence of a Protein Can Be Determined by Mass Spectrometry

5.4j. Sequence Databases Contain the Amino Acid Sequences of Millions of Different Proteins

5.5. What Is the Nature of Amino Acid Sequences?

5.5a. Homologous Proteins from Different Organisms Have Homologous Amino Acid Sequences

5.5b. Computer Programs Can Align Sequences and Discover Homology between Proteins

5.5c. Related Proteins Share a Common Evolutionary Origin

5.5d. Apparently Different Proteins May Share a Common Ancestry

5.5e. A Mutant Protein Is a Protein with a Slightly Different Amino Acid Sequence

5.6. Can Polypeptides Be Synthesized in the Laboratory?

5.6a. Solid-Phase Methods Are Very Useful in Peptide Synthesis

5.7. Do Proteins Have Chemical Groups Other than Amino Acids?

5.8. What Are the Many Biological Functions of Proteins?

All Proteins Function through Specific Recognition and Binding of Some Target Molecule

5.9. What Is the Proteome and What Does It Tell Us?

5.9a. The Proteome Is Dynamic

5.9b. Determining the Proteome of a Cell

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 6. Proteins: Secondary, Tertiary, and Quaternary Structure

6.1. What Noncovalent Interactions Stabilize the Higher Levels of Protein Structure?

6.1a. Hydrogen Bonds Are Formed whenever Possible

6.1b. Hydrophobic Interactions Drive Protein Folding

6.1c. Ionic Interactions Usually Occur on the Protein Surface

6.1d. Van der Waals Interactions Are Ubiquitous

6.2. What Role Does the Amino Acid Sequence Play in Protein Structure?

6.3. What Are the Elements of Secondary Structure in Proteins, and How Are They Formed?

6.3a. All Protein Structure Is Based on the Amide Plane

6.3b. The Alpha-Helix Is a Key Secondary Structure

6.3c. The β -Pleated Sheet Is a Core Structure in Proteins

6.3d. Helix–Sheet Composites in Spider Silk

6.3e. β -Turns Allow the Protein Strand to Change Direction

6.4. How Do Polypeptides Fold into Three-Dimensional Protein Structures?

6.4a. Fibrous Proteins Usually Play a Structural Role

6.4b. Globular Proteins Mediate Cellular Function

6.4c. Helices and Sheets Make up the Core of Most Globular Proteins

6.4d. Waters on the Protein Surface Stabilize the Structure

6.4e. Packing Considerations

6.4f. Protein Domains Are Nature’s Modular Strategy for Protein Design

6.4g. Classification Schemes for the Protein Universe Are Based on Domains

6.4h. Denaturation Leads to Loss of Protein Structure and Function

6.4i. Anfinsen’s Classic Experiment Proved that Sequence Determines Structure

6.4j. Is There a Single Mechanism for Protein Folding?

6.4k. What Is the Thermodynamic Driving Force for Folding of Globular Proteins?

6.4l. Marginal Stability of the Tertiary Structure Makes Proteins Flexible

6.4m. Motion in Globular Proteins

6.4n. The Folding Tendencies and Patterns of Globular Proteins

6.4o. Most Globular Proteins Belong to One of Four Structural Classes

6.4p. Molecular Chaperones Are Proteins that Help other Proteins to Fold

6.4q. Some Proteins Are Intrinsically Unstructured

6.5. How Do Protein Subunits Interact at the Quaternary Level of Protein Structure?

6.5a. There Is Symmetry in Quaternary Structures

6.5b. Quaternary Association Is Driven by Weak Forces

6.5c. Open Quaternary Structures Can Polymerize

6.5d. There Are Structural and Functional Advantages to Quaternary Association

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 7. Carbohydrates and the Glycoconjugates of Cell Surfaces

7.1. How Are Carbohydrates Named?

7.2. What Are the Structure and Chemistry of Monosaccharides?

7.2a. Monosaccharides Are Classified as Aldoses and Ketoses

7.2b. Stereochemistry Is a Prominent Feature of Monosaccharides

7.2c. Monosaccharides Exist in Cyclic and Anomeric Forms

7.2d. Haworth Projections Are a Convenient Device for Drawing Sugars

7.2e. Monosaccharides Can Be Converted to Several Derivative Forms

7.3. What Are the Structure and Chemistry of Oligosaccharides?

7.3a. Disaccharides Are the Simplest Oligosaccharides

7.3b. A Variety of Higher Oligosaccharides Occur in Nature

7.4. What Are the Structure and Chemistry of Polysaccharides?

7.4a. Nomenclature for Polysaccharides Is Based on Their Composition and Structure

7.4b. Polysaccharides Serve Energy Storage, Structure, and Protection Functions

7.4c. Polysaccharides Provide Stores of Energy

7.4d. Polysaccharides Provide Physical Structure and Strength to Organisms

7.4e. Polysaccharides Provide Strength and Rigidity to Bacterial Cell Walls

7.4f. Peptidoglycan Is the Polysaccharide of Bacterial Cell Walls

7.4g. Animals Display a Variety of Cell Surface Polysaccharides

7.5. What Are Glycoproteins, and How Do They Function in Cells?

7.5a. Carbohydrates on Proteins Can Be O-Linked or N-Linked

7.5b. O-GlcNAc Signaling Is Altered in Diabetes and Cancer

7.5c. O-Linked Saccharides Form Rigid Extended Extracellular Structures

7.5d. Polar Fish Depend on Antifreeze Glycoproteins

7.5e. N-Linked Oligosaccharides Can Affect the Physical Properties and Functions of a Protein

7.5f. Sialic Acid Terminates the Oligosaccharides of Glycoproteins and Glycolipids

7.5g. Sialic Acid Cleavage Can Serve as a Timing Device for Protein Degradation

7.6. How Do Proteoglycans Modulate Processes in Cells and Organisms?

7.6a. Functions of Proteoglycans Involve Binding to Other Proteins

7.6b. Proteoglycans May Modulate Cell Growth Processes

7.6c. Proteoglycans Make Cartilage Flexible and Resilient

7.7. Do Carbohydrates Provide a Structural Code?

7.7a. Lectins Translate the Sugar Code

7.7b. Selectins, Rolling Leukocytes, and the Inflammatory Response

7.7c. Galectins—Mediators of Inflammation, Immunity, and Cancer

7.7d. C-Reactive Protein—A Lectin that Limits Inflammation Damage

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 8. Lipids

8.1. What Are the Structures and Chemistry of Fatty Acids?

8.2. What Are the Structures and Chemistry of Triacylglycerols?

8.3. What Are the Structures and Chemistry of Glycerophospholipids?

8.3a. Glycerophospholipids Are the Most Common Phospholipids

8.3b. Ether Glycerophospholipids Include PAF and Plasmalogens

8.4. What Are Sphingolipids, and How Are They Important for Higher Animals?

8.5. What Are Waxes, and How Are They Used?

8.6. What Are Terpenes, and What Is Their Relevance to Biological Systems?

The Membranes of Archaea Are Rich in Isoprene-Based Lipids

8.7. What Are Steroids, and What Are Their Cellular Functions?

8.7a. Cholesterol

8.7b. Steroid Hormones Are Derived from Cholesterol

8.8. How Do Lipids and Their Metabolites Act as Biological Signals?

8.9. What Can Lipidomics Tell Us about Cell, Tissue, and Organ Physiology?

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 9. Membranes and Membrane Transport

9.1. What Are the Chemical and Physical Properties of Membranes?

9.1a. The Composition of Membranes Suits Their Functions

9.1b. Lipids Form Ordered Structures Spontaneously in Water

9.1c. The Fluid Mosaic Model Describes Membrane Dynamics

9.2. What Are the Structure and Chemistry of Membrane Proteins?

9.2a. Peripheral Membrane Proteins Associate Loosely with the Membrane

9.2b. Integral Membrane Proteins Are Firmly Anchored in the Membrane

9.2c. Lipid-Anchored Membrane Proteins Are Switching Devices

9.3. How Are Biological Membranes Organized?

9.3a. Membranes Are Asymmetric and Heterogeneous Structures

9.4. What Are the Dynamic Processes That Modulate Membrane Function?

9.4a. Lipids and Proteins Undergo a Variety of Movements in Membranes

9.4b. Membrane Lipids Can Be Ordered to Different Extents

9.5. How Does Transport Occur across Biological Membranes?

9.6. What Is Passive Diffusion?

9.6a. Charged Species May Cross Membranes by Passive Diffusion

9.7. How Does Facilitated Diffusion Occur?

9.7a. Membrane Channel Proteins Facilitate Diffusion

9.7b. The B. cereus Na ⁢ K Channel Uses a Variation on the K + Selectivity Filter

9.7c. CorA Is a Pentameric Mg 2 + Channel

9.7d. Chloride, Water, Glycerol, and Ammonia Flow through Single-Subunit Pores

9.8. How Does Energy Input Drive Active Transport Processes?

9.8a. All Active Transport Systems Are Energy-Coupling Devices

9.8b. Many Active Transport Processes Are Driven by ATP

9.8c. ABC Transporters Use ATP to Drive Import and Export Functions and Provide Multidrug Resistance

9.9. How Are Certain Transport Processes Driven by Light Energy?

9.9a. Bacteriorhodopsin Uses Light Energy to Drive Proton Transport

9.10. How Is Secondary Active Transport Driven by Ion Gradients?

9.10a. Na + and H + Drive Secondary Active Transport

9.10b. AcrB Is a Secondary Active Transport System

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 10. Nucleotides and Nucleic Acids

10.1. What Are the Structure and Chemistry of Nitrogenous Bases?

10.1a. Three Pyrimidines and Two Purines Are Commonly Found in Cells

10.1b. The Properties of Pyrimidines and Purines Can Be Traced to Their Electron-Rich Nature

10.2. What Are Nucleosides?

10.3. What Are the Structure and Chemistry of Nucleotides?

10.3a. Cyclic Nucleotides Are Cyclic Phosphodiesters

10.3b. Nucleoside Diphosphates and Triphosphates Are Nucleotides with Two or Three Phosphate Groups

10.3c. NDPs and NTPs Are Polyprotic Acids

10.3d. Nucleoside 5 ′ -Triphosphates Are Carriers of Chemical Energy

10.4. What Are Nucleic Acids?

10.4a. The Base Sequence of a Nucleic Acid Is Its Defining Characteristic

10.5. What Are the Different Classes of Nucleic Acids?

10.5a. The Fundamental Structure of DNA Is a Double Helix

10.5b. Various Forms of RNA Serve Different Roles in Cells

10.5c. The Chemical Differences between DNA and RNA Have Biological Significance

10.6. Are Nucleic Acids Susceptible to Hydrolysis?

10.6a. RNA Is Susceptible to Hydrolysis by Base, but DNA Is Not

10.6b. The Enzymes that Hydrolyze Nucleic Acids Are Phosphodiesterases

10.6c. Nucleases Differ in Their Specificity for Different Forms of Nucleic Acid

10.6d. Restriction Enzymes Are Nucleases that Cleave Double-Stranded DNA Molecules

10.6e. Type II Restriction Endonucleases Are Useful for Manipulating DNA in the Lab

10.6f. Restriction Endonucleases Can Be Used to Map the Structure of a DNA Fragment

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 11. Structure of Nucleic Acids

11.1. How Do Scientists Determine the Primary Structure of Nucleic Acids?

11.1a. The Nucleotide Sequence of DNA Can Be Determined from the Electrophoretic Migration of a Defined Set of Polynucleotide Fragments

11.1b. Sanger’s Chain Termination or Dideoxy Method Uses DNA Replication to Generate a Defined Set of Polynucleotide Fragments

11.1c. Next-Generation Sequencing

11.1d. High-Throughput DNA Sequencing by the Light of Fireflies

11.1e. Illumina Next-Gen Sequencing

11.1f. Emerging Technologies to Sequence DNA Are Based on Single-Molecule Sequencing Strategies

11.2. What Sorts of Secondary Structures Can Double-Stranded DNA Molecules Adopt?

11.2a. Conformational Variation in Polynucleotide Strands

11.2b. DNA Usually Occurs in the Form of Double-Stranded Molecules

11.2c. Watson–Crick Base Pairs Have Virtually Identical Dimensions

11.2d. The DNA Double Helix Is a Stable Structure

11.2e. Double Helical Structures Can Adopt a Number of Stable Conformations

11.2f. A-Form DNA Is an Alternative Form of Right-Handed DNA

11.2g. Z-DNA Is a Conformational Variation in the Form of a Left-Handed Double Helix

11.2h. The Double Helix Is a Very Dynamic Structure

11.2i. Alternative Hydrogen-Bonding Interactions Give Rise to Novel DNA Structures: Cruciforms, Triplexes, and Quadruplexes

11.3. Can the Secondary Structure of DNA Be Denatured and Renatured?

11.3a. Thermal Denaturation of DNA Can Be Observed by Changes in UV Absorbance

11.3b. pH Extremes or Strong H -Bonding Solutes also Denature DNA Duplexes

11.3c. Single-Stranded DNA Can Renature to Form DNA Duplexes

11.3d. The Rate of DNA Renaturation Is an Index of DNA Sequence Complexity

11.3e. Nucleic Acid Hybridization: Different DNA Strands of Similar Sequence Can Form Hybrid Duplexes

11.4. Can DNA Adopt Structures of Higher Complexity?

11.4a. Supercoils Are One Kind of Structural Complexity in DNA

11.5. What Is the Structure of Eukaryotic Chromosomes?

11.5a. Nucleosomes Are the Fundamental Structural Unit in Chromatin

11.5b. Higher-Order Structural Organization of Chromatin Gives Rise to Chromosomes

11.5c. SMC Proteins Establish Chromosome Organization and Mediate Chromosome Dynamics

11.6. Can Nucleic Acids Be Synthesized Chemically?

11.6a. Phosphoramidite Chemistry Is Used to Form Oligonucleotides from Nucleotides

11.6b. Genes Can Be Synthesized Chemically

11.7. What Are the Secondary and Tertiary Structures of RNA?

11.7a. Transfer RNA Adopts Higher-Order Structure through Intrastrand Base Pairing

11.7b. Messenger RNA Adopts Higher-Order Structure through Intrastrand Base Pairing

11.7c. Ribosomal RNA Also Adopts Higher-Order Structure through Intrastrand Base Pairing

11.7d. Aptamers Are Oligonucleotides Specifically Selected for Their Ligand-Binding Ability

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 12. Recombinant DNA, Cloning, Chimeric Genes, and Synthetic Biology

12.1. What Does It Mean “To Clone”?

12.1a. Plasmids Are Very Useful in Cloning Genes

12.1b. Shuttle Vectors Are Plasmids that Can Propagate in Two Different Organisms

12.1c. Artificial Chromosomes Can Be Created from Recombinant DNA

12.2. What Is a DNA Library?

12.2a. Genomic Libraries Are Prepared from the Total DNA in an Organism

12.2b. Libraries Can Be Screened for the Presence of Specific Genes

12.2c. Probes for Screening Libraries Can Be Prepared in a Variety of Ways

12.2d. PCR Is Used to Clone and Amplify Specific Genes

12.2e. cDNA Libraries Are DNA Libraries Prepared from mRNA

12.2f. DNA Microarrays (Gene Chips) Are Arrays of Different Oligonucleotides Immobilized on a Chip

12.3. Can the Cloned Genes in Libraries Be Expressed?

12.3a. Expression Vectors Are Engineered so that the RNA or Protein Products of Cloned Genes Can Be Expressed

12.3b. Reporter Gene Constructs Are Chimeric DNA Molecules Composed of Gene Regulatory Sequences Positioned next to an Easily Expressible Gene Product

12.3c. Specific Protein–Protein Interactions Can Be Identified Using the Yeast Two-Hybrid System

12.3d. In Vitro Mutagenesis

12.4. How Is RNA Interference Used to Reveal the Function of Genes?

12.4a. RNAi Using Synthetic shRNAs

12.5. How Does High-Throughput Technology Allow Global Study of Millions of Genes or Molecules at Once?

12.5a. High-Throughput Screening

12.5b. DNA Laser Printing

12.5c. High-Throughput RNAi Screening of Mammalian Genomes

12.5d. High-Throughput Protein Screening

12.6. Is It Possible to Make Directed Changes in the Heredity of an Organism?

12.6a. Human Gene Therapy Can Repair Genetic Deficiencies

12.6b. Viruses as Vectors in Human Gene Therapy

12.7. What Is the New Field of Synthetic Biology?

12.7a. DNA as Code

12.7b. iGEM and BioBricks (Registry of Standard Biological Parts)

12.7c. Metabolic Engineering

12.7d. Genome Engineering

12.7e. Genome Editing with CRISPR/Cas9

12.7f. Synthetic Genomes

Summary

Foundational Biochemistry

Problems

Further Reading

Part II. Protein Dynamics

Chapter 13. Enzymes—Kinetics and Specificity

13.1. What Characteristic Features Define Enzymes?

13.1a. Catalytic Power Is Defined as the Ratio of the Enzyme-Catalyzed Rate of a Reaction to the Uncatalyzed Rate

13.1b. Specificity Is the Term Used to Define the Selectivity of Enzymes for Their Substrates

13.1c. Regulation of Enzyme Activity Ensures That the Rate of Metabolic Reactions Is Appropriate to Cellular Requirements

13.1d. Enzyme Nomenclature Provides a Systematic Way of Naming Metabolic Reactions

13.1e. Coenzymes and Cofactors Are Nonprotein Components Essential to Enzyme Activity

13.2. Can the Rate of an Enzyme-Catalyzed Reaction Be Defined in a Mathematical Way?

13.2a. Chemical Kinetics Provides a Foundation for Exploring Enzyme Kinetics

13.2b. Bimolecular Reactions Are Reactions Involving Two Reactant Molecules

13.2c. Catalysts Lower the Free Energy of Activation for a Reaction

13.2d. Decreasing Δ G ‡ Increases Reaction Rate

13.3. What Equations Define the Kinetics of Enzyme-Catalyzed Reactions?

13.3a. The Substrate Binds at the Active Site of an Enzyme

13.3b. The Michaelis–Menten Equation Is the Fundamental Equation of Enzyme Kinetics

13.3c. Assume That [ES] Remains Constant during an Enzymatic Reaction

13.3d. Assume That Velocity Measurements Are Made Immediately after Adding S

13.3e. The Michaelis Constant, K m , Is Defined as ( k – 1 + k 2 ) / k 1

13.3f. When [ S ] = K m , v = V max / 2

13.3g. Plots of v versus [S] Illustrate the Relationships between V max , K m , and Reaction Order

13.3h. Turnover Number Defines the Activity of One Enzyme Molecule

13.3i. The Ratio, k cat / K m , Defines the Catalytic Efficiency of an Enzyme

13.3j. Linear Plots Can Be Derived from the Michaelis–Menten Equation

13.3k. Nonlinear Lineweaver–Burk or Hanes–Woolf Plots Are a Property of Regulatory Enzymes

13.3l. Enzymatic Activity Is Strongly Influenced by pH

13.3m. The Response of Enzymatic Activity to Temperature Is Complex

13.4. What Can Be Learned from the Inhibition of Enzyme Activity?

13.4a. Enzymes May Be Inhibited Reversibly or Irreversibly

13.4b. Reversible Inhibitors May Bind at the Active Site or at Some Other Site

13.4c. Enzymes Also Can Be Inhibited in an Irreversible Manner

13.5. What Is the Kinetic Behavior of Enzymes Catalyzing Bimolecular Reactions?

13.5a. The Conversion of AEB to PEQ Is the Rate-Limiting Step in Random, Single-Displacement Reactions

13.5b. In an Ordered, Single-Displacement Reaction, the Leading Substrate Must Bind First

13.5c. Double-Displacement (Ping-Pong) Reactions Proceed via Formation of a Covalently Modified Enzyme Intermediate

13.5d. Exchange Reactions Are One Way to Diagnose Bisubstrate Mechanisms

13.5e. Multisubstrate Reactions Can Also Occur in Cells

13.6. How Can Enzymes Be so Specific?

13.6a. The “Lock and Key” Hypothesis Was the First Explanation for Specificity

13.6b. The “Induced Fit” Hypothesis Provides a More Accurate Description of Specificity

13.6c. “Induced Fit” Favors Formation of the Transition State

13.6d. Specificity and Reactivity

13.7. Are All Enzymes Proteins?

13.7a. RNA Molecules That Are Catalytic Have Been Termed “Ribozymes”

13.7b. Antibody Molecules Can Have Catalytic Activity

13.8. Is It Possible to Design an Enzyme to Catalyze Any Desired Reaction?

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 14. Mechanisms of Enzyme Action

14.1. What Are the Magnitudes of Enzyme-Induced Rate Accelerations?

14.2. What Role Does Transition-State Stabilization Play in Enzyme Catalysis?

14.3. How Does Destabilization of ES Affect Enzyme Catalysis?

14.4. How Tightly Do Transition-State Analogs Bind to the Active Site?

14.5. What Are the Mechanisms of Catalysis?

14.5a. Enzymes Facilitate Formation of Near-Attack Conformations

14.5b. Protein Motions Are Essential to Enzyme Catalysis

14.5c. Covalent Catalysis

14.5d. General Acid–Base Catalysis

14.5e. Low-Barrier Hydrogen Bonds

14.5f. Quantum Mechanical Tunneling in Electron and Proton Transfers

14.5g. Metal Ion Catalysis

14.6. What Can Be Learned from Typical Enzyme Mechanisms?

14.6a. Serine Proteases

14.6b. The Digestive Serine Proteases

14.6c. The Chymotrypsin Mechanism in Detail: Kinetics

14.6d. The Serine Protease Mechanism in Detail: Events at the Active Site

14.6e. The Aspartic Proteases

14.6f. The Mechanism of Action of Aspartic Proteases

14.6g. The AIDS Virus HIV-1 Protease Is an Aspartic Protease

14.6h. Chorismate Mutase: A Model for Understanding Catalytic Power and Efficiency

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 15. Enzyme Regulation

15.1. What Factors Influence Enzymatic Activity?

15.1a. The Availability of Substrates and Cofactors Usually Determines How Fast the Reaction Goes

15.1b. As Product Accumulates, the Apparent Rate of the Enzymatic Reaction Will Decrease

15.1c. Genetic Regulation of Enzyme Synthesis and Decay Determines the Amount of Enzyme Present at Any Moment

15.1d. Enzyme Activity Can Be Regulated Allosterically

15.1e. Enzyme Activity Can Be Regulated through Covalent Modification

15.1f. Regulation of Enzyme Activity Also Can Be Accomplished in Other Ways

15.1g. Zymogens Are Inactive Precursors of Enzymes

15.1h. Isozymes Are Enzymes with Slightly Different Subunits

15.2. What Are the General Features of Allosteric Regulation?

15.2a. Regulatory Enzymes Have Certain Exceptional Properties

15.3. Can Allosteric Regulation Be Explained by Conformational Changes in Proteins?

15.3a. The Symmetry Model for Allosteric Regulation Is Based on Two Conformational States for a Protein

15.3b. The Sequential Model for Allosteric Regulation Is Based on Ligand-Induced Conformational Changes

15.3c. Changes in the Oligomeric State of a Protein Can Also Give Allosteric Behavior

15.4. What Kinds of Covalent Modification Regulate the Activity of Enzymes?

15.4a. Covalent Modification through Reversible Phosphorylation

15.4b. Protein Kinases: Target Recognition and Intrasteric Control

15.4c. Phosphorylation Is Not the Only Form of Covalent Modification That Regulates Protein Function

15.4d. Acetylation Is a Prominent Modification for the Regulation of Metabolic Enzymes

15.5. Is the Activity of Some Enzymes Controlled by both Allosteric Regulation and Covalent Modification?

15.5a. The Glycogen Phosphorylase Reaction Converts Glycogen into Readily Usable Fuel in the Form of Glucose-1-Phosphate

15.5b. Glycogen Phosphorylase Is a Homodimer

15.5c. Glycogen Phosphorylase Activity Is Regulated Allosterically

15.5d. Covalent Modification of Glycogen Phosphorylase Trumps Allosteric Regulation

15.5e. Enzyme Cascades Regulate Glycogen Phosphorylase Covalent Modification

Special Focus. Is There an Example in Nature That Exemplifies the Relationship between Quaternary Structure and the Emergence of Allosteric Properties? Hemoglobin and Myoglobin—Paradigms of Protein Structure and Function

The Comparative Biochemistry of Myoglobin and Hemoglobin Reveals Insights into Allostery

Myoglobin Is an Oxygen-Storage Protein

O 2 Binds to the Mb Heme Group

O 2 Binding Alters Mb Conformation

Cooperative Binding of Oxygen by Hemoglobin Has Important Physiological Significance

Hemoglobin Has an α 2 ‍ β 2 Tetrameric Structure

Oxygenation Markedly Alters the Quaternary Structure of Hb

Movement of the Heme Iron by less than 0.04 nm Induces the Conformational Change in Hemoglobin

The Oxy and Deoxy Forms of Hemoglobin Represent Two Different Conformational States

The Allosteric Behavior of Hemoglobin Has both Symmetry (MWC) Model and Sequential (KNF) Model Components

H + Promotes the Dissociation of Oxygen from Hemoglobin

CO 2 Also Promotes the Dissociation of O 2 from Hemoglobin

2,3-Bisphosphoglycerate Is an Important Allosteric Effector for Hemoglobin

BPG Binding to Hb Has Important Physiological Significance

Fetal Hemoglobin Has a Higher Affinity for O 2 because It Has a Lower Affinity for BPG

Sickle-Cell Anemia Is Characterized by Abnormal Red Blood Cells

Sickle-Cell Anemia Is a Molecular Disease

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 16. Molecular Motors

16.1. What Is a Molecular Motor?

16.2. What Is the Molecular Mechanism of Muscle Contraction?

16.2a. Muscle Contraction Is Triggered by Ca 2 + Release from Intracellular Stores

16.2b. The Molecular Structure of Skeletal Muscle Is Based on Actin and Myosin

16.2c. The Mechanism of Muscle Contraction Is Based on Sliding Filaments

16.3. What Are the Molecular Motors That Orchestrate the Mechanochemistry of Microtubules?

16.3a. Filaments of the Cytoskeleton Are Highways That Move Cellular Cargo

16.3b. Three Classes of Motor Proteins Move Intracellular Cargo

16.3c. Dyneins Move Organelles in a Plus-to-Minus Direction; Kinesins, in a Minus-to-Plus Direction—Mostly

16.3d. Cytoskeletal Motors Are Highly Processive

16.3e. ATP Binding and Hydrolysis Drive Hand-over-Hand Movement of Kinesin

16.3f. The Conformation Change That Leads to Movement Is Different in Myosins and Dyneins

16.4. How Do Molecular Motors Unwind DNA?

16.4a. Negative Cooperativity Facilitates Hand-over-Hand Movement

16.4b. Papillomavirus E1 Helicase Moves along DNA on a Spiral Staircase

16.5. How Do Bacterial Flagella Use a Proton Gradient to Drive Rotation?

16.5a. The Flagellar Rotor Is a Complex Structure

16.5b. Gradients of H + and Na + Drive Flagellar Rotors

16.5c. The Flagellar Rotor Self-Assembles in a Spontaneous Process

16.5d. Flagellar Filaments Are Composed of Protofilaments of Flagellin

16.5e. Motor Reversal Involves Conformation Switching of Motor and Filament Proteins

Summary

Foundational Biochemistry

Problems

Further Reading

Part III. Metabolism and Its Regulation

Chapter 17. Metabolism: An Overview

17.1. Is Metabolism Similar in Different Organisms?

17.1a. Living Things Exhibit Metabolic Diversity

17.1b. Oxygen Is Essential to Life for Aerobes

17.1c. The Flow of Energy in the Biosphere and the Carbon and Oxygen Cycles Are Intimately Related

17.2. What Can Be Learned from Metabolic Maps?

17.2a. The Metabolic Map Can Be Viewed as a Set of Dots and Lines

17.2b. Alternative Models Can Provide New Insights into Pathways

17.2c. Multienzyme Systems May Take Different Forms

17.3. How Do Anabolic and Catabolic Processes Form the Core of Metabolic Pathways?

17.3a. Anabolism Is Biosynthesis

17.3b. Anabolism and Catabolism Are Not Mutually Exclusive

17.3c. The Pathways of Catabolism Converge to a Few End Products

17.3d. Anabolic Pathways Diverge, Synthesizing an Astounding Variety of Biomolecules from a Limited Set of Building Blocks

17.3e. Amphibolic Intermediates Play Dual Roles

17.3f. Corresponding Pathways of Catabolism and Anabolism Differ in Important Ways

17.3g. ATP Serves in a Cellular Energy Cycle

17.3h. NAD + Collects Electrons Released in Catabolism

17.3i. NADPH Provides the Reducing Power for Anabolic Processes

17.3j. Coenzymes and Vitamins Provide Unique Chemistry and Essential Nutrients to Pathways

17.4. What Experiments Can Be Used to Elucidate Metabolic Pathways?

17.4a. Mutations Create Specific Metabolic Blocks

17.4b. Isotopic Tracers Can Be Used as Metabolic Probes

17.4c. NMR Spectroscopy Is a Noninvasive Metabolic Probe

17.4d. Metabolic Pathways Are Compartmentalized within Cells

17.5. What Can the Metabolome Tell Us about a Biological System?

Discovery Metabolomics

17.6. What Food Substances Form the Basis of Human Nutrition?

17.6a. Humans Require Protein

17.6b. Carbohydrates Provide Metabolic Energy

17.6c. Lipids Are Essential, but in Moderation

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 18. Glycolysis

18.1. What Are the Essential Features of Glycolysis?

18.2. Why Are Coupled Reactions Important in Glycolysis?

18.3. What Are the Chemical Principles and Features of the First Phase of Glycolysis?

18.3a. Reaction 1: Glucose Is Phosphorylated by Hexokinase or Glucokinase—The First Priming Reaction

18.3b. Reaction 2: Phosphoglucoisomerase Catalyzes the Isomerization of Glucose-6-Phosphate

18.3c. Reaction 3: ATP Drives a Second Phosphorylation by Phosphofructokinase—The Second Priming Reaction

18.3d. Reaction 4: Cleavage by Fructose Bisphosphate Aldolase Creates Two 3-Carbon Intermediates

18.3e. Reaction 5: Triose Phosphate Isomerase Completes the First Phase of Glycolysis

18.4. What Are the Chemical Principles and Features of the Second Phase of Glycolysis?

18.4a. Reaction 6: Glyceraldehyde-3-Phosphate Dehydrogenase Creates a High-Energy Intermediate

18.4b. Reaction 7: Phosphoglycerate Kinase Is the Break-Even Reaction

18.4c. Reaction 8: Phosphoglycerate Mutase Catalyzes a Phosphoryl Transfer

18.4d. Reaction 9: Dehydration by Enolase Creates PEP

18.4e. Reaction 10: Pyruvate Kinase Yields More ATP

18.5. What Are the Metabolic Fates of NADH and Pyruvate Produced in Glycolysis?

18.5a. Anaerobic Metabolism of Pyruvate Leads to Lactate or Ethanol

18.5b. Lactate Accumulates under Anaerobic Conditions in Animal Tissues

18.5c. The Old Shell Game—How Turtles Survive the Winter

18.6. How Do Cells Regulate Glycolysis?

18.7. Are Substrates Other than Glucose Used in Glycolysis?

18.7a. Fructose Catabolism in Liver is Unregulated—and Potentially Harmful

18.7b. Mannose Enters Glycolysis in Two Steps

18.7c. Galactose Enters Glycolysis via the Leloir Pathway

18.7d. An Enzyme Deficiency Causes Lactose Intolerance

18.7e. Glycerol Can Also Enter Glycolysis

18.8. How Do Cells Respond to Hypoxic Stress?

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 19. The Tricarboxylic Acid Cycle

19.1. What Is the Chemical Logic of the TCA Cycle?

19.1a. The TCA Cycle Provides a Chemically Feasible Way of Cleaving a Two-Carbon Compound

19.2. How Is Pyruvate Oxidatively Decarboxylated to Acetyl-CoA?

19.3. How Are Two CO 2 Molecules Produced from Acetyl-CoA?

19.3a. The Citrate Synthase Reaction Initiates the TCA Cycle

19.3b. Citrate Is Isomerized by Aconitase to Form Isocitrate

19.3c. Isocitrate Dehydrogenase Catalyzes the First Oxidative Decarboxylation in the Cycle

19.3d. α -Ketoglutarate Dehydrogenase Catalyzes the Second Oxidative Decarboxylation of the TCA Cycle

19.4. How Is Oxaloacetate Regenerated to Complete the TCA Cycle?

19.4a. Succinyl-CoA Synthetase Catalyzes Substrate-Level Phosphorylation

19.4b. Succinate Dehydrogenase Is FAD-Dependent

19.4c. Fumarase Catalyzes the Trans-Hydration of Fumarate to Form L -Malate

19.4d. Malate Dehydrogenase Completes the Cycle by Oxidizing Malate to Oxaloacetate

19.5. What Are the Energetic Consequences of the TCA Cycle?

19.5a. The Carbon Atoms of Acetyl-CoA Have Different Fates in the TCA Cycle

19.6. Can the TCA Cycle Provide Intermediates for Biosynthesis?

19.7. What Are the Anaplerotic, or “Filling Up,” Reactions?

19.8. How Is the TCA Cycle Regulated?

19.8a. Pyruvate Dehydrogenase Is Regulated by Phosphorylation/Dephosphorylation

19.8b. Isocitrate Dehydrogenase Is Strongly Regulated

19.8c. Regulation of TCA Cycle Enzymes by Acetylation

19.8d. Two Covalent Modifications Regulate E. coli Isocitrate Dehydrogenase

19.8e. The TCA Cycle Operates as a Metabolon

19.9. Can Any Organisms Use Acetate as Their Sole Carbon Source?

19.9a. The Glyoxylate Cycle Operates in Specialized Organelles

19.9b. Isocitrate Lyase Short-Circuits the TCA Cycle by Producing Glyoxylate and Succinate

19.9c. The Glyoxylate Cycle Helps Plants Grow in the Dark

19.9d. Glyoxysomes Must Borrow Three Reactions from Mitochondria

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 20. Electron Transport and Oxidative Phosphorylation

20.1. Where in the Cell Do Electron Transport and Oxidative Phosphorylation Occur?

20.1a. Mitochondrial Functions Are Localized in Specific Compartments

20.1b. The Mitochondrial Matrix Contains the Enzymes of the TCA Cycle

20.2. How Is the Electron-Transport Chain Organized?

20.2a. The Electron-Transport Chain Can Be Isolated in Four Complexes

20.2b. Complex I Oxidizes NADH and Reduces Coenzyme Q

20.2c. Complex II Oxidizes Succinate and Reduces Coenzyme Q

20.2d. Complex III Mediates Electron Transport from Coenzyme Q to Cytochrome c

20.2e. Complex IV Transfers Electrons from Cytochrome c to Reduce Oxygen on the Matrix Side

20.2f. Proton Transport across Cytochrome c Oxidase Is Coupled to Oxygen Reduction

20.2g. The Complexes of Electron Transport May Function as Supercomplexes

20.2h. Electron Transfer Energy Stored in a Proton Gradient: The Mitchell Hypothesis

20.3. What Are the Thermodynamic Implications of Chemiosmotic Coupling?

20.4. How Does a Proton Gradient Drive the Synthesis of ATP?

20.4a. ATP Synthase Is Composed of F 1 and F 0

20.4b. The Catalytic Sites of ATP Synthase Adopt Three Different Conformations

20.4c. Boyer’s O 18 Exchange Experiment Identified the Energy-Requiring Step

20.4d. Boyer’s Binding Change Mechanism Describes the Events of Rotational Catalysis

20.4e. Proton Flow through F 0 Drives Rotation of the Motor and Synthesis of ATP

20.4f. How Many Protons Are Required to Make an ATP? It Depends on the Organism

20.4g. Racker and Stoeckenius Confirmed the Mitchell Model in a Reconstitution Experiment

20.4h. Inhibitors of Oxidative Phosphorylation Reveal Insights about the Mechanism

20.4i. Uncouplers Disrupt the Coupling of Electron Transport and ATP Synthase

20.4j. ATP–ADP Translocase Mediates the Movement of ATP and ADP across the Mitochondrial Membrane

20.5. What Is the P/O Ratio for Mitochondrial Oxidative Phosphorylation?

20.6. How Are the Electrons of Cytosolic NADH Fed into Electron Transport?

20.6a. The Glycerophosphate Shuttle Ensures Efficient Use of Cytosolic NADH

20.6b. The Malate–Aspartate Shuttle Is Reversible

20.6c. The Net Yield of ATP from Glucose Oxidation Depends on the Shuttle Used

20.6d. 3.5 Billion Years of Evolution Have Resulted in a Very Efficient System

20.7. How Do Mitochondria Mediate Apoptosis?

20.7a. Cytochrome c Triggers Apoptosome Assembly

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 21. Photosynthesis

21.1. What Are the General Properties of Photosynthesis?

21.1a. Photosynthesis Occurs in Membranes

21.1b. Photosynthesis Consists of both Light Reactions and Dark Reactions

21.1c. Water Is the Ultimate e – Donor for Photosynthetic NADP + Reduction

21.2. How Is Solar Energy Captured by Chlorophyll?

21.2a. Chlorophylls and Accessory Light-Harvesting Pigments Absorb Light of Different Wavelengths

21.2b. The Light Energy Absorbed by Photosynthetic Pigments Has Several Possible Fates

21.2c. The Transduction of Light Energy into Chemical Energy Involves Oxidation–Reduction

21.2d. Photosynthetic Units Consist of Many Chlorophyll Molecules but Only a Single Reaction Center

21.3. What Kinds of Photosystems Are Used to Capture Light Energy?

21.3a. Chlorophyll Exists in Plant Membranes in Association with Proteins

21.3b. PSI and PSII Participate in the Overall Process of Photosynthesis

21.3c. The Pathway of Photosynthetic Electron Transfer Is Called the Z Scheme

21.3d. Oxygen Evolution Requires the Accumulation of Four Oxidizing Equivalents in PSII

21.3e. Electrons Are Taken from H 2 O to Replace Electrons Lost from P680

21.3f. Electrons from PSII Are Transferred to PSI via the Cytochrome b 6 f Complex

21.3g. Plastocyanin Transfers Electrons from the Cytochrome b 6 f Complex to PSI

21.4. What Is the Molecular Architecture of Photosynthetic Reaction Centers?

21.4a. The R. viridis Photosynthetic Reaction Center Is an Integral Membrane Protein

21.4b. Photosynthetic Electron Transfer by the R. viridis Reaction Center Leads to ATP Synthesis

21.4c. The Molecular Architecture of PSII Resembles the R. viridis Reaction Center Architecture

21.4d. How Does PSII Generate O 2 from H 2 O ?

21.4e. The Molecular Architecture of PSI Resembles the R. viridis Reaction Center and PSII Architecture

21.4f. How Do Green Plants Carry out Photosynthesis?

21.5. What Is the Quantum Yield of Photosynthesis?

21.5a. Calculation of the Photosynthetic Energy Requirements for Hexose Synthesis Depends on H + / h υ and ATP / H + Ratios

21.6. How Does Light Drive the Synthesis of ATP?

21.6a. The Mechanism of Photophosphorylation Is Chemiosmotic

21.6b. CF 1 CF 0 –ATP Synthase Is the Chloroplast Equivalent of the Mitochondrial F 1 F 0 –ATP Synthase

21.6c. Photophosphorylation Can Occur in either a Noncyclic or a Cyclic Mode

21.6d. Cyclic Photophosphorylation Generates ATP but Not NADPH or O 2

21.7. How Is Carbon Dioxide Used to Make Organic Molecules?

21.7a. Ribulose-1,5-Bisphosphate Is the CO 2 Acceptor in CO 2 Fixation

21.7b. 2-Carboxy-3-Keto-Arabinitol Is an Intermediate in the Ribulose-1,5-Bisphosphate Carboxylase Reaction

21.7c. Ribulose-1,5-Bisphosphate Carboxylase Exists in Inactive and Active Forms

21.7d. CO 2 Fixation into Carbohydrate Proceeds via the Calvin–Benson Cycle

21.7e. The Enzymes of the Calvin Cycle Serve Three Metabolic Purposes

21.7f. The Calvin Cycle Reactions Can Account for Net Hexose Synthesis

21.7g. The Carbon Dioxide Fixation Pathway Is Indirectly Activated by Light

21.7h. Protein–Protein Interactions Mediated by an Intrinsically Unstructured Protein Also Regulate Calvin–Benson Cycle Activity

21.8. How Does Photorespiration Limit CO 2 Fixation?

21.8a. Tropical Grasses Use the Hatch–Slack Pathway to Capture Carbon Dioxide for CO 2 Fixation

21.8b. Cacti and Other Desert Plants Capture CO 2 at Night

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 22. Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

22.1. What Is Gluconeogenesis, and How Does It Operate?

22.1a. The Substrates for Gluconeogenesis Include Pyruvate, Lactate, and Amino Acids

22.1b. Nearly All Gluconeogenesis Occurs in the Liver and Kidneys in Animals

22.1c. Gluconeogenesis Is Not Merely the Reverse of Glycolysis

22.1d. Gluconeogenesis—Something Borrowed, Something New

22.1e. Four Reactions Are Unique to Gluconeogenesis

22.2. How Is Gluconeogenesis Regulated?

22.2a. Gluconeogenesis Is Regulated by Allosteric and Substrate-Level Control Mechanisms

22.2b. Substrate Cycles Provide Metabolic Control Mechanisms

22.3. How Are Glycogen and Starch Catabolized in Animals?

22.3a. Dietary Starch Breakdown Provides Metabolic Energy

22.3b. Metabolism of Tissue Glycogen Is Regulated

22.4. How Is Glycogen Synthesized?

22.4a. Glucose Units Are Activated for Transfer by Formation of Sugar Nucleotides

22.4b. UDP–Glucose Synthesis Is Driven by Pyrophosphate Hydrolysis

22.4c. Glycogen Synthase Catalyzes Formation of α ( 1 → 4 ) Glycosidic Bonds in Glycogen

22.4d. Glycogen Branching Occurs by Transfer of Terminal Chain Segments

22.5. How Is Glycogen Metabolism Controlled?

22.5a. Glycogen Metabolism Is Highly Regulated

22.5b. Glycogen Synthase Is Regulated by Covalent Modification

22.5c. Hormones Regulate Glycogen Synthesis and Degradation

22.6. Can Glucose Provide Electrons for Biosynthesis?

22.6a. The Pentose Phosphate Pathway Operates Mainly in Liver and Adipose Cells

22.6b. The Pentose Phosphate Pathway Begins with Two Oxidative Steps

22.6c. There Are Four Nonoxidative Reactions in the Pentose Phosphate Pathway

22.6d. Utilization of Glucose-6-P Depends on the Cell’s Need for ATP, NADPH, and Ribose-5-P

22.6e. Xylulose-5-Phosphate Is a Metabolic Regulator

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 23. Fatty Acid Catabolism

23.1. How Are Fats Mobilized from Dietary Intake and Adipose Tissue?

23.1a. Modern Diets Are Often High in Fat

23.1b. Triacylglycerols Are a Major Form of Stored Energy in Animals

23.1c. Hormones Trigger the Release of Fatty Acids from Adipose Tissue

23.1d. Degradation of Dietary Triacylglycerols Occurs Primarily in the Duodenum

23.2. How Are Fatty Acids Broken Down?

23.2a. Knoop Elucidated the Essential Feature of β -Oxidation

23.2b. Coenzyme A Activates Fatty Acids for Degradation

23.2c. Carnitine Carries Fatty Acyl Groups across the Inner Mitochondrial Membrane

23.2d. β -Oxidation Involves a Repeated Sequence of Four Reactions

23.2e. Repetition of the β -Oxidation Cycle Yields a Succession of Acetate Units

23.2f. Complete β -Oxidation of One Palmitic Acid Yields 106 Molecules of ATP

23.2g. Migratory Birds Travel Long Distances on Energy from Fatty Acid Oxidation

23.2h. Fatty Acid Oxidation Is an Important Source of Metabolic Water for Some Animals

23.3. How Are Odd-Carbon Fatty Acids Oxidized?

23.3a. β -Oxidation of Odd-Carbon Fatty Acids Yields Propionyl-CoA

23.3b. A B 12 -Catalyzed Rearrangement Yields Succinyl-CoA from L -Methylmalonyl-CoA

23.3c. Net Oxidation of Succinyl-CoA Requires Conversion to Acetyl-CoA

23.4. How Are Unsaturated Fatty Acids Oxidized?

23.4a. An Isomerase and a Reductase Facilitate the β -Oxidation of Unsaturated Fatty Acids

23.4b. Degradation of Polyunsaturated Fatty Acids Requires 2,4-Dienoyl-CoA Reductase

23.5. Are There Other Ways to Oxidize Fatty Acids?

23.5a. Peroxisomal β -Oxidation Requires FAD-Dependent Acyl-CoA Oxidase

23.5b. Branched-Chain Fatty Acids Are Degraded via α -Oxidation

23.5c. ω -Oxidation of Fatty Acids Yields Small Amounts of Dicarboxylic Acids

23.6. What Are Ketone Bodies, and What Role Do They Play in Metabolism?

23.6a. Ketone Bodies Are a Significant Source of Fuel and Energy for Certain Tissues

23.6b. β -Hydroxybutyrate Is a Signaling Metabolite

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 24. Lipid Biosynthesis

24.1. How Are Fatty Acids Synthesized?

24.1a. Formation of Malonyl-CoA Activates Acetate Units for Fatty Acid Synthesis

24.1b. Fatty Acid Biosynthesis Depends on the Reductive Power of NADPH

24.1c. Cells Must Provide Cytosolic Acetyl-CoA and Reducing Power for Fatty Acid Synthesis

24.1d. Acetate Units Are Committed to Fatty Acid Synthesis by Formation of Malonyl-CoA

24.1e. Acetyl-CoA Carboxylase Is Biotin Dependent and Displays Ping-Pong Kinetics

24.1f. Acetyl-CoA Carboxylase in Animals Is a Multifunctional Protein

24.1g. Phosphorylation of ACC Modulates Activation by Citrate and Inhibition by Palmitoyl-CoA

24.1h. Acyl Carrier Proteins Carry the Intermediates in Fatty Acid Synthesis

24.1i. In Some Organisms, Fatty Acid Synthesis Takes Place in Multienzyme Complexes

24.1j. Decarboxylation Drives the Condensation of Acetyl-CoA and Malonyl-CoA

24.1k. Reduction of the β -Carbonyl Group Follows a Now-Familiar Route

24.1l. Eukaryotes Build Fatty Acids on Megasynthase Complexes

24.1m. C 16 Fatty Acids May Undergo Elongation and Unsaturation

24.1n. Unsaturation Reactions Occur in Eukaryotes in the Middle of an Aliphatic Chain

24.1o. The Unsaturation Reaction May Be Followed by Chain Elongation

24.1p. Mammals Cannot Synthesize Most Polyunsaturated Fatty Acids

24.1q. Arachidonic Acid Is Synthesized from Linoleic Acid by Mammals

24.1r. Regulatory Control of Fatty Acid Metabolism Is an Interplay of Allosteric Modifiers and Phosphorylation–Dephosphorylation Cycles

24.1s. Hormonal Signals Regulate ACC and Fatty Acid Biosynthesis

24.2. How Are Complex Lipids Synthesized?

24.2a. Glycerolipids Are Synthesized by Phosphorylation and Acylation of Glycerol

24.2b. Eukaryotes Synthesize Glycerolipids from CDP-Diacylglycerol or Diacylglycerol

24.2c. Phosphatidylethanolamine Is Synthesized from Diacylglycerol and CDP-Ethanolamine

24.2d. Exchange of Ethanolamine for Serine Converts Phosphatidylethanolamine to Phosphatidylserine

24.2e. Eukaryotes Synthesize Other Phospholipids via CDP-Diacylglycerol

24.2f. Dihydroxyacetone Phosphate Is a Precursor to the Plasmalogens

24.2g. Platelet-Activating Factor Is Formed by Acetylation of 1-Alkyl-2-Lysophosphatidylcholine

24.2h. Sphingolipid Biosynthesis Begins with Condensation of Serine and Palmitoyl-CoA

24.2i. Ceramide Is the Precursor for Other Sphingolipids and Cerebrosides

24.3. How Are Eicosanoids Synthesized, and What Are Their Functions?

24.3a. Eicosanoids Are Local Hormones

24.3b. Prostaglandins Are Formed from Arachidonate by Oxidation and Cyclization

24.3c. A Variety of Stimuli Trigger Arachidonate Release and Eicosanoid Synthesis

24.3d. “Take Two Aspirin and …” Inhibit Your Prostaglandin Synthesis

24.4. How Is Cholesterol Synthesized?

24.4a. Mevalonate Is Synthesized from Acetyl-CoA via HMG-CoA Synthase

24.4b. A Thiolase Brainteaser Asks why Thiolase Can’t Be Used in Fatty Acid Synthesis

24.4c. Squalene Is Synthesized from Mevalonate

24.4d. Conversion of Lanosterol to Cholesterol Requires 20 Additional Steps

24.5. How Are Lipids Transported throughout the Body?

24.5a. Lipoprotein Complexes Transport Triacylglycerols and Cholesterol Esters

24.5b. Lipoproteins in Circulation Are Progressively Degraded by Lipoprotein Lipase

24.5c. The Structure of the LDL Receptor Involves Five Domains

24.5d. The LDL Receptor β -Propellor Displaces LDL Particles in Endosomes

24.5e. Defects in Lipoprotein Metabolism Can Lead to Elevated Serum Cholesterol

24.6. How Are Bile Acids Biosynthesized?

24.7. How Are Steroid Hormones Synthesized and Utilized?

24.7a. Pregnenolone and Progesterone Are the Precursors of All Other Steroid Hormones

24.7b. Steroid Hormones Modulate Transcription in the Nucleus

24.7c. Cortisol and Other Corticosteroids Regulate a Variety of Body Processes

24.7d. Anabolic Steroids Have Been Used Illegally to Enhance Athletic Performance

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 25. Nitrogen Acquisition and Amino Acid Metabolism

25.1. Which Metabolic Pathways Allow Organisms to Live on Inorganic Forms of Nitrogen?

25.1a. Nitrogen Is Cycled between Organisms and the Inanimate Environment

25.1b. Nitrate Assimilation Is the Principal Pathway for Ammonium Biosynthesis

25.1c. Organisms Gain Access to Atmospheric N 2 via the Pathway of Nitrogen Fixation

25.2. What Is the Metabolic Fate of Ammonium?

25.2a. The Major Pathways of Ammonium Assimilation Lead to Glutamine Synthesis

25.3. What Regulatory Mechanisms Act on Escherichia coli Glutamine Synthetase?

25.3a. Glutamine Synthetase Is Allosterically Regulated

25.3b. Glutamine Synthetase Is Regulated by Covalent Modification

25.3c. Glutamine Synthetase Is Regulated through Gene Expression

25.3d. Glutamine in the Human Body

25.4. How Do Organisms Synthesize Amino Acids?

25.4a. Amino Acids Are Formed from α -Keto Acids by Transamination

25.4b. The Pathways of Amino Acid Biosynthesis Can Be Organized into Families

25.4c. The α -Ketoglutarate Family of Amino Acids Includes Glu, Gln, Pro, Arg, and Lys

25.4d. The Urea Cycle Acts to Excrete Excess N through Arg Breakdown

25.4e. The Oxaloacetate Family of Amino Acids Includes Asp, Asn, Lys, Met, Thr, and Ile

25.4f. The Pyruvate Family of Amino Acids Includes Ala, Val, and Leu

25.4g. The 3-Phosphoglycerate Family of Amino Acids Includes Ser, Gly, and Cys

25.4h. The Aromatic Amino Acids Are Synthesized from Chorismate

25.4i. Histidine Biosynthesis and Purine Biosynthesis Are Connected by Common Intermediates

25.5. How Does Amino Acid Catabolism Lead into Pathways of Energy Production?

25.5a. The 20 Common Amino Acids Are Degraded by 20 Different Pathways that Converge to Just 7 Metabolic Intermediates

25.5b. Animals Differ in the Form of Nitrogen that They Excrete

Summary

Foundational Biochemistry

Problems

Further Reading

Chapter 26. Synthesis and Degradation of Nucleotides

Part IV. Information Transfer

Chapter 28. DNA Metabolism: Replication, Recombination, and Repair

Chapter 29. Transcription and the Regulation of Gene Expression

Chapter 30. Protein Synthesis

Chapter 32. The Reception and Transmission of Extracellular Information

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