Chapter 1: Biochemistry Concepts and Themes

1.1 Science and the Scientific Method

• What is Science?
• What is the Scientific Method?

1.2 Organisms, Cells, Chromosomes, and Genes

• Organisms Belong to Three Distinct Domains of Life
• Cells Are the Structural and Functional Units of All Living Organisms
• Viruses Cannot Live Independently of Cells
• Bacterial Cells Feature a Relatively Simple Architecture and Streamlined Lifestyles
• Eukaryotic Cells Have a Variety of Membranous Organelles
• Cells Contain a Wide Range of Supramolecular Structures
• Major Model Organisms and Systems are Useful in Biochemistry
• The Linear Sequence in DNA Encodes Proteins with Three-Dimensional Structures

1.3 The Organic Chemistry of Biochemistry

• Major Organic Species are Found in Cells
• Macromolecules Are the Major Constituents of Cells
• Molecular Weight and Molecular Mass are Expressed by Distinct Conventions
• Nucleophiles and Electrophiles Define How Many Reactions Proceed
• Cofactors Facilitate Particular Classes of Biochemical Reactions

1.4 A Review of Basic Thermodynamics

• Equilibrium Constants and Rate Constants Describe Distinct but Related Thermodynamic Parameters
• Organisms Transform Energy and Matter from Their Surroundings
• Creating and Maintaining Order Requires Work and Energy

1.5 Using Data Banks

Chapter 2: Water: The Chemistry of Life

2.1 Weak Interactions in Aqueous Systems

• Hydrogen Bonds Give Water Its Unusual Properties
• Water Interacts Electrostatically with Charged Solutes
• Nonpolar Gases Are Poorly Soluble in Water
• The Hydrophobic Effect is an Entropy-based Phenomenon
• van der Waals Interactions and Other Weak Interactions Are Key to Macromolecular Structure and Function

2.2 Ionization of Water, Weak Acids, and Weak Bases

• The Ionization of Water Is Expressed by an Equilibrium Constant
• The pH Scale Designates H+ and OH- Concentrations
• Weak Acids and Bases Have Characteristic Acid Dissociation Constants
• Titration Curves Reveal the pKa of Weak Acids

2.3 Buffering against pH Changes in Biological Systems

• A Buffer System Resists Changes in pH in Response to Added Acid or Base.
• The Henderson-Hasselbalch Equation Relates pH, pKa, and Buffer Concentration
• Weak Acids or Bases Buffer Cells and Tissues against pH Changes
• Phosphate and Bicarbonate Are Important Biological Buffer Systems Untreated Diabetes Produces Life-Threatening Acidosis

Chapter 3: Amino Acids, Peptides, and Proteins

3.1 Amino Acids

• What is an Amino Acid?
• The Amino Acid Residues in Proteins Are L Stereoisomers
• Amino Acids Can Be Classified by R Group
• Some Amino Acids Absorb Ultraviolet Light
• Uncommon Amino Acids Also Have Important Functions
• Amino Acids Can Act as Acids and Bases
• Amino Acids Differ in Their Acid-Base Properties

3.2 Peptides and Proteins

• Peptides Are Chains of Amino Acids
• Disulfide Bonds Occur in Some Proteins
• Ionization Behavior Can Distinguish Peptides
• Some Proteins Contain Chemical Groups Other Than Amino Acids

3.3 Purifying Proteins

• Proteins Can Be Separated and Purified
• Proteins Are Detected and Quantified Based on Their Functions
• Proteins Can Be Separated and Characterized by Electrophoresis

3.4 The Primary Structure of Proteins and Protein Chemistry

• There are Levels of Complexity to Protein Structure
• The Function of a Protein Depends on Its Amino Acid Sequence
• There are Multiple Ways to Reduce a Polypeptide Chain into Fragments.
• Mass Spectrometry Provides Information on Molecular Mass, Amino Acid Sequence, and Entire Proteomes
• Amino Acid Sequences Provide Important Biochemical and Evolutionary Information

Chapter 4: Protein Structure

4.1 Forces and Interactions that Stabilize Protein Structures

• Protein Structures Are Largely Stabilized by Weak Interactions
• Hydrogen Bonding, Ion Pairs, and van der Waals Interactions Also Contribute to Protein Folding
• The Conformation of the Peptide Bond Constrains Polypeptide Conformation

4.2 Secondary Protein Structure

• The ¿ Helix Maximizes the Use of Polypeptide Hydrogen Bonds
• The ß Strand is a Common Secondary Structure with an Extended Conformation
• Ramachandran Plots Describe the Distribution of Secondary Structure in a Protein

4.3 Tertiary and Quaternary Protein Structure

• Fibrous Proteins Have a Single Type of Secondary Structure
• The Fibrous Protein Collagen is the Most Abundant Protein in Mammals
• Silk is Made from a Fibrous Protein with b-sheet Secondary Structure
• Globular Proteins are Compact and Highly Varied in Three Dimensional Structure
• Protein Tertiary Structures can be Described in Terms of Motifs and Domains.
• Intrinsically Disordered Proteins Lack Stable Tertiary Structures.
• Quaternary Structure Describes the Organization of Multisubunit Proteins.
• Biomolecular Structures Can be Determined Using a Variety of Methods
• The Protein Data Bank is a Repository for Biomolecular Structures

4.4 Protein Denaturation and Folding

• Loss of Protein Structure Results in Loss of Function
• Amino Acid Sequence Determines Tertiary Structure
• Protein Folding Occurs by Defined Pathways and can be Assisted by Chaperones.
• Defects in Protein Folding Cause Human Disease

Chapter 5: Protein Function and Ligand Binding

5.1 Reversible Protein-Ligand Binding

• Ligands Bind to Proteins Reversibly at Binding Sites
• Protein-Ligand Interactions Can Be Described Quantitatively

5.2 Reversible Binding of a Protein to a Ligand: Oxygen-Binding by Myoglobin

• Oxygen Can Bind to a Heme Prosthetic Group
• Globins Are a Family of Oxygen-Binding Proteins
• The Binding of Oxygen to Myoglobin can be Described Quantitatively
• Protein Structure Affects How Ligands Bind

5.3 Reversible and Cooperative Binding of a Protein to a Ligand: Oxygen-Binding by Hemoglobin

• Hemoglobin Subunits Are Structurally Similar to Myoglobin
• Hemoglobin Undergoes a Structural Change on Binding Oxygen
• Hemoglobin Binds Oxygen Cooperatively
• Cooperative Ligand Binding Can Be Described Quantitatively
• Hemoglobin Also Transports H+ and CO2

5.4 Medical Conditions Related to Hemoglobin

• CO Binding to Hemoglobin Poses a Serious Health Risk
• Altered Hemoglobin Subunit Interactions in Sickle Cell Anemia Cause Pain and Suffering

Chapter 6: Protein Function and Enzymes

6.1 What are Enzymes?

• Most Enzymes Are Proteins
• Enzyme-catalyzed Reactions Occur Within Active Sites
• Enzymes Affect Reaction Rates, Not Equilibria
• Reaction Rates and Equilibria are Described by Constants

6.2 How Enzymes Work

• Noncovalent Interactions between Enzyme and Substrate Are Optimized in the Transition State
• Enzymes Use a Variety of Additional Chemical Mechanisms to Facilitate Catalysis
• Coenzymes Facilitate Particular Types of Reactions

6.3 Enzyme Kinetics

• The Steady State of an Enzyme-catalyzed Reaction Reflects the Concentration of ES
• The Relationship Between Substrate Concentration and Reaction Rate can be Described Quantitatively
• Scientists Compare Enzymes Using Vmax and Km.
• Enzymes are Subject to Reversible and Irreversible Inhibition

6.4 Chymotrypsin and Enzymatic Catalysis

• The Chymotrypsin Mechanism Involves Acylation and Deacylation of an Active Site Ser Residue
• An Understanding of Protease Mechanisms Led to Treatments for HIV
• An Understanding of Enzyme Mechanism Leads to Useful Antibiotics

6.5 Regulatory Enzymes

• Some Enzymes are Regulated by Allosteric Conformational Changes in Response to Modulator Binding
• Some Enzymes are Regulated by Reversible Covalent Modification
• Some Enzymes are Regulated by Proteolytic Cleavage of an Enzyme Precursor

Chapter 7: Carbohydrates

7.1 Monosaccharides and Disaccharides

• The Two Families of Monosaccharides Are Aldoses and Ketoses
• The Common Monosaccharides Have Cyclic Structures
• Sugars Containing and Forming Aldehydes are Reducing Sugars
• Disaccharides Consist of Two Monosaccharides Joined by a Glycosidic Bond

7.2 Polysaccharides

• Some Homopolysaccharides Are Storage Forms of Fuel While Others have Structural Roles
• Glycosaminoglycans Are Heteropolysaccharides of the Extracellular Matrix

7.3 Glycoconjugates: Peptidoglycans, Proteoglycans, Glycoproteins, and Glycolipids

• Peptidoglycan Reinforces the Bacterial Cell Wall
• Proteoglycans Are Glycosaminoglycan-Containing Macromolecules of the Cell Surface and Extracellular Matrix
• Glycoproteins Are Proteins with Covalently Attached Oligosaccharides
• Glycolipids and Lipopolysaccharides Are Membrane Components

7.4 Carbohydrates as Signaling Molecules

• Oligosaccharides Have Highly Diverse Structures
• Lectins Are Proteins That Bind Specifically to Complex Oligosaccharides and Mediate Many Biological Processes

Chapter 8: Lipids, Membranes, and Membrane Proteins

8.1 Membrane Lipids

• Fatty Acids are the...