Biochemistry 9/e

Chapter 1 Biochemistry: An Evolving Science
1.1 Biochemical Unity Underlies Biological Diversity
1.2 DNA Illustrates the Interplay Between Form and Function
DNA is constructed from four building blocks
Two single strands of DNA combine to form a double helix
DNA structure explains heredity and the storage of information
1.3 Concepts from Chemistry Explain the Properties of Biological Molecules
The formation of the DNA double helix as a key example
The double helix can form from its component strands
Covalent and noncovalent bonds are important for the structure and stability of biological molecules
The double helix is an expression of the rules of chemistry
The laws of thermodynamics govern the behavior of biochemical systems
Heat is released in the formation of the double helix
Acid–base reactions are central in many biochemical processes
Acid–base reactions can disrupt the double helix
Buffers regulate pH in organisms and in the laboratory
1.4 The Genomic Revolution Is Transforming Biochemistry, Medicine, and Other Fields
Genome sequencing has transformed biochemistry and other fields
Environmental factors influence human biochemistry
Genome sequences encode proteins and patterns of expression
APPENDIX  Visualizing Molecular Structures: Small Molecules
APPENDIX  Functional Groups

Chapter 2 Protein Composition and Structure
2.1 Proteins Are Built from a Repertoire of 20 Amino Acids
2.2 Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains
Proteins have unique amino acid sequences specified by genes
Polypeptide chains are flexible yet conformationally restricted
2.3 Secondary Structure: Polypeptide Chains Can Fold into Regular Structures Such As the Alpha Helix, the Beta Sheet, and Turns and Loops
The alpha helix is a coiled structure stabilized by intrachain hydrogen bonds
Beta sheets are stabilized by hydrogen bonding between polypeptide strands
Polypeptide chains can change direction by making reverse turns and loops
2.4 Tertiary Structure: Proteins Can Fold into Globular or Fibrous Structures
Fibrous proteins provide structural support for cells and tissues
2.5 Quaternary Structure: Polypeptide Chains Can Assemble into Multisubunit Structures
2.6 The Amino Acid Sequence of a Protein Determines Its Three-Dimensional Structure
Amino acids have different propensities for forming < helices, ® sheets, and turns
Protein folding is a highly cooperative process
Proteins fold by progressive stabilization of intermediates rather than by random search
Prediction of three-dimensional structure from sequence remains a great challenge
Some proteins are inherently unstructured and can exist in multiple conformations
Protein misfolding and aggregation are associated with some neurological diseases
Posttranslational modifications confer new capabilities to proteins
APPENDIX  Visualizing Molecular Structures: Proteins

Chapter 3 Exploring Proteins and Proteomes
3.1 The Purification of Proteins Is an Essential First Step in Understanding Their Function
The assay: How do we recognize the protein that we are looking for?
Proteins must be released from the cell to be purified
Proteins can be purified according to solubility, size, charge, and binding affinity
Proteins can be separated by gel electrophoresis and displayed
A protein purification scheme can be quantitatively evaluated
Ultracentrifugation is valuable for separating biomolecules and determining their masses
Protein purification can be made easier with the use of recombinant DNA technology
3.2 Immunology Provides Important Techniques with Which to Investigate Proteins
Antibodies to specific proteins can be generated
Monoclonal antibodies with virtually any desired specificity can be readily prepared
Proteins can be detected and quantified by using an enzyme-linked immunosorbent assay
Western blotting permits the detection of proteins separated by gel electrophoresis
Co-immunoprecipitation enables the identification of binding partners of a protein
Fluorescent markers make the visualization of proteins in the cell possible
3.3 Mass Spectrometry Is a Powerful Technique for the Identification of Peptides and Proteins
Peptides can be sequenced by mass spectrometry
Proteins can be specifically cleaved into small peptides to facilitate analysis
Genomic and proteomic methods are complementary
The amino acid sequence of a protein provides valuable information
Individual proteins can be identified by mass spectrometry
3.4 Peptides Can Be Synthesized by Automated Solid-Phase Methods
3.5 Three-Dimensional Protein Structure Can Be Determined by X-ray Crystallography, NMR Spectroscopy, and Cryo-Electron Microscopy
X-ray crystallography reveals three-dimensional structure in atomic detail
Nuclear magnetic resonance spectroscopy can reveal the structures of proteins in solution  
Cryo-electron microscopy is an emerging method of protein structure determination
APPENDIX  Problem-Solving Strategies

Chapter 4 DNA, RNA, and the Flow of Genetic Information
4.1 A Nucleic Acid Consists of Four Kinds of Bases Linked to a Sugar–Phosphate Backbone
RNA and DNA differ in the sugar component and one of the bases
Nucleotides are the monomeric units of nucleic acids
DNA molecules are very long and have directionality
4.2 A Pair of Nucleic Acid Strands with Complementary Sequences Can Form a Double-Helical Structure
The double helix is stabilized by hydrogen bonds and van der Waals interactions
DNA can assume a variety of structural forms 
Some DNA molecules are circular and supercoiled
Single-stranded nucleic acids can adopt elaborate structures
4.3 The Double Helix Facilitates the Accurate Transmission of Hereditary Information
Differences in DNA density established the validity of the semiconservative replication hypothesis
The double helix can be reversibly melted
Unusual circular DNA exists in the eukaryotic nucleus
4.4 DNA Is Replicated by Polymerases That Take Instructions from Templates
DNA polymerase catalyzes phosphodiester-bridge formation
The genes of some viruses are made of RNA
4.5 Gene Expression Is the Transformation of DNA Information into Functional Molecules
Several kinds of RNA play key roles in gene expression
All cellular RNA is synthesized by RNA polymerases
RNA polymerases take instructions from DNA templates
Transcription begins near promoter sites and ends at terminator sites
Transfer RNAs are the adaptor molecules in protein synthesis
4.6 Amino Acids Are Encoded by Groups of Three Bases Starting from a Fixed Point
Major features of the genetic code
Messenger RNA contains start and stop signals for protein synthesis
The genetic code is nearly universal
4.7 Most Eukaryotic Genes Are Mosaics of Introns and Exons
RNA processing generates mature RNA
Many exons encode protein domains
APPENDIX  Problem-Solving Strategies
Chapter 5 Exploring Genes and Genomes
5.1 The Exploration of Genes Relies on Key Tools
Restriction enzymes split DNA into specific fragments
Restriction fragments can be separated by gel electrophoresis and visualized
DNA can be sequenced by controlled termination of replication