Foundations of General Organic and Biochemistry

Title
Contents
1 Chemistry: Methods and Measurement
	1.1 The Discovery Process
		Chemistry
		The Scientific Method
	A Lifestyle Connection The Scientific Method
		Models in Chemistry
	A Medical Connection Curiosity, Science, and Medicine
	1.2 Matter and Properties
		Physical Properties
		Chemical Properties
		Intensive and Extensive Properties
		Classification of Matter
	1.3 Measurement in Chemistry
		Data, Results, and Units
		English and Metric Units
		Unit Conversion: English and Metric Systems
		Conversion of Units Within the Same System
		Conversion of Units from One System to Another
	1.4 Significant Figures and Scientific Notation
		Significant Figures
		Recognition of Significant Figures
		Scientific Notation
		Error, Accuracy, Precision, and Uncertainty
		Significant Figures in Calculation of Results
		Exact (Counted) and Inexact Numbers
		Rounding Off Numbers
	1.5 Experimental Quantities
		Mass
		Length
		Volume
		Time
		Temperature
		Density and Specific Gravity
	A Medical Connection Diagnosis Based on Waste
2 The Structure of the Atom and the Periodic Table
	2.1 Composition of the Atom
		Electrons, Protons, and Neutrons
		Isotopes
	Chemistry at the Crime Scene Microbial Forensics
		Ions
	2.2 Development of Atomic Theory
		Dalton’s Theory
		Evidence for Subatomic Particles: Electrons, Protons, and Neutrons
		Evidence for the Nucleus
	2.3 The Periodic Law and the Periodic Table
		Numbering Groups in the Periodic Table
		Periods and Groups
		Metals and Nonmetals
		Atomic Number and Atomic Mass
	2.4 Electron Arrangement and the Periodic Table
		Valence Electrons
	A Medical Connection Copper Deficiency and Wilson’s Disease
		The Quantum Mechanical Atom
			Energy Levels and Sublevels
			Electron Configuration and the Aufbau Principle
			Shorthand Electron Configurations
	2.5 The Octet Rule
		Ion Formation and the Octet Rule
	2.6 Trends in the Periodic Table
		Atomic Size
		Ion Size
		Ionization Energy
		Electron Affinity
	A Medical Connection Dietary Calcium
3 Structure and Properties of Ionic and Covalent Compounds
	3.1 Chemical Bonding
		Lewis Symbols
		Principal Types of Chemical Bonds: Ionic and Covalent
		Polar Covalent Bonding and Electronegativity
	3.2 Naming Compounds and Writing Formulas of Compounds
		Ionic Compounds
		Covalent Compounds
	3.3 Properties of Ionic and Covalent Compounds
	A Lifestyle Connection Origin of the Elements
		Physical State
			Melting and Boiling Points
			Structure of Compounds in the Solid State
			Solutions of Ionic and Covalent Compounds
	3.4 Drawing Lewis Structures of Molecules
		AStrategy for Drawing Lewis Structures of Molecules
	A Medical Connection Blood Pressure and the Sodium Ion/Potassium Ion Ratio
		Multiple Bonds and Bond Energies
			Lewis Structures and Exceptions to the Octet Rule
			Lewis Structures and Molecular Geometry; VSEPR Theory
			Lewis Structures and Polarity
	3.5 Properties Based on Electronic Structure and Molecular Geometry
		Solubility
		Boiling Points of Liquids and Melting Points of Solids
4 Calculations and the Chemical Equation
	4.1 The Mole Concept and Atoms
		The Mole and Avogadro’s Number
		Calculating Atoms, Moles, and Mass
	4.2 The Chemical Formula, Formula Weight, and Molar Mass
		The Chemical Formula
		Formula Weight and Molar Mass
	4.3 Chemical Equations and the Information They Convey
		A Recipe for Chemical Change
		Features of a Chemical Equation
		The Experimental Basis of a Chemical Equation
		Writing Chemical Reactions
		Types of Chemical Reactions
	4.4 Balancing Chemical Equations
	A Medical Connection Carbon Monoxide Poisoning: A Case of Combining Ratios
	4.5 Calculations Using a Chemical Equation
		General Principles
		Use of Conversion Factors
	A Lifestyle Connection The Chemistry of Automobile Air Bags
		Theoretical and Percent Yield
	A Medical Connection Pharmaceutical Chemistry: The Practical Significance of Percent Yield
5 Energy, Rate, and Equilibrium
	5.1 Energy, Work, and Heat
		Energy: The Basics
		Thermodynamics
		The Chemical Reaction and Energy
		Exothermic and Endothermic Reactions
	A Medical Connection Hot and Cold Packs
		Enthalpy
		Spontaneous and Nonspontaneous Reactions
		Entropy
	A Lifestyle Connection Triboluminescence: Sparks in the Dark with Candy
	5.2 Experimental Determination of Energy Change in Reactions
	A Lifestyle Connection Food Calories
	A Lifestyle Connection The Cost of Energy? More Than You Imagine
	5.3 Kinetics
		The Chemical Reaction
		Activation Energy and the Activated Complex
		Factors That Affect Reaction Rate
	5.4 Equilibrium
		Rate and Reversibility of Reactions
		Chemical Equilibrium
		LeChatelier ’s Principle
6 States of Matter: Gases, Liquids, and Solids
	6.1 The Gaseous State
		Ideal Gas Concept
		Description of a Gas
		Kinetic Molecular Theory of Gases
		Properties of Gases and the Kinetic Molecular Theory
		Boyle’s Law: Relationship of Pressure and Volume
		Charles’s Law: Relationship of Temperature and Volume
		Combined Gas Law
		Avogadro’s Law: Relationship of Number of Moles and Volume
		Molar Volume of a Gas
		Gas Densities
		The Ideal Gas Law
		Dalton’s Law of Partial Pressures
	An Environmental Perspective The Greenhouse Effect and Global Warming
		Ideal Gases Versus Real Gases
	6.2 The Liquid State
		Compressibility
		Viscosity
	A Medical Connection Blood Gases and Respiration
		Surface Tension
		Vapor Pressure of a Liquid
	Chemistry at the Crime Scene Explosives at the Airport
		van der Waals Forces
		Hydrogen Bonding
	6.3 The Solid State
		Properties of Solids
		Types of Crystalline Solids
	A Lifestyle Connection An Extraordinary Molecule
7 Solutions
	7.1 Properties of Solutions
		General Properties of Liquid Solutions
		Solutions and Colloids
		Degree of Solubility
		Solubility and Equilibrium
		Solubility of Gases: Henry’s Law
	7.2 Concentration Based on Mass
		Weight/Volume Percent
	A Lifestyle Connection Scuba Diving: Nitrogen and the Bends
		Weight/Weight Percent
		Parts Per Thousand (ppt) and Parts Per Million (ppm)
	7.3 Concentration Based on Moles
		Molarity
		Dilution
	7.4 Concentration-Dependent Solution Properties
		Vapor Pressure Lowering
		Freezing Point Depression and Boiling Point Elevation
		Osmotic Pressure
	A Medical Connection Oral Rehydration Therapy
	7.5 Water as a Solvent
	7.6 Electrolytes in Body Fluids
		Representation of Concentration of Ions in Solution
		Blood: An Ionic Solution and More
	A Medical Connection Hemodialysis
8 Acids and Bases
	8.1 Acids and Bases
		Arrhenius Theory of Acids and Bases
		Brønsted-Lowry Theory of Acids and Bases
		Acid-Base Properties of Water
		Acid and Base Strength
		Conjugate Acids and Bases
		The Dissociation of Water
	8.2 pH: A Measurement Scale for Acids and Bases
		A Definition of pH
		Measuring pH
		Calculating pH
	A Medical Connection Drug Delivery
		The Importance of pH and pH Control
	8.3 Reactions Between Acids and Bases
		Neutralization
	An Environmental Perspective Acid Rain
		Polyprotic Substances
	8.4 Acid-Base Buffers
		The Buffer Process
		Addition of Base (OH�) to a Buffer Solution
		Addition of Acid (H3O�) to a Buffer Solution
	A Medical Connection Control of Blood pH
9 The Nucleus and Radioactivity
	9.1 Natural Radioactivity
		Alpha Particles
		Beta Particles and Positrons
		Gamma Rays
		Properties of Alpha, Beta, and Gamma Radiation
	A Lifestyle Connection An Extraordinary Woman in Science
	9.2 Writing a Balanced Nuclear Equation
		Alpha Decay
		Beta Decay
		Positron Emission
		Gamma Production
		Predicting Products of Nuclear Decay
	9.3 Properties of Radioisotopes
		Nuclear Structure and Stability
		Half-Life
	9.4 Nuclear Power
		Energy Production
		Nuclear Fission
	An Environmental Perspective Nuclear Waste Disposal
		Nuclear Fusion
		Breeder Reactors
	9.5 Medical Applications of Radioactivity
	A Lifestyle Connection Radiocarbon Dating
		Cancer Therapy Using Radiation
		Nuclear Medicine
	A Medical Connection Magnetic Resonance Imaging
		Making Isotopes for Medical Applications
	9.6 Biological Effects of Radiation
		Radiation Exposure and Safety
	An Environmental Perspective Radon and Indoor Air Pollution
	9.7 Measurement of Radiation
		Nuclear Imaging
		Computer Imaging
		The Geiger Counter
		Film Badges
		Units of Radiation Measurement
10 An Introduction to Organic Chemistry: The Saturated Hydrocarbons
	10.1 The Chemistry of Carbon
		Important Differences Between Organic and Inorganic Compounds
	An Environmental Perspective Frozen Methane: Treasure or Threat?
		Families of Organic Compounds
	10.2 Alkanes
		Structure and Physical Properties
			Alkyl Groups
			Nomenclature
			Constitutional or Structural Isomers
	10.3 Cycloalkanes
	An Environmental Perspective The Petroleum Industry and Gasoline Production
	10.4 Reactions of Alkanes and Cycloalkanes
		Combustion
	Chemistry at the Crime Scene Arson and Alkanes
		Halogenation
	A Medical Connection Polyhalogenated Hydrocarbons Used as Anesthetics
11 The Unsaturated Hydrocarbons: Alkenes, Alkynes, and Aromatics
	11.1 Alkenes and Alkynes: Structure and Physical Properties
	11.2 Alkenes and Alkynes: Nomenclature
		A Medical Connection Killer Alkynes in Nature
	11.3 Geometric Isomers
	An Environmental Perspective Alkenes in Nature
		Cis-Trans Isomers in the Diet
	11.4 Reactions Involving Alkenes and Alkynes
		Hydrogenation: Addition of H2
		Halogenation: Addition of X2
		Hydration: Addition of H2O
	A Lifestyle Connection Life Without Polymers?
		Addition Polymers of Alkenes
	11.5 Aromatic Hydrocarbons
		Structure and Properties
		Nomenclature
		Polycyclic Aromatic Hydrocarbons
	11.6 Heterocyclic Aromatic Compounds
12 Oxygen- and Sulfur- Containing Organic Compounds
	12.1 Alcohols
		Structure and Physical Properties
		Nomenclature
		Medically Important Alcohols
		Classification of Alcohols
		Reactions Involving Alcohols
	Chemistry at the Crime Scene Fingerprinting
	Chemistry at the Crime Scene Drinking and Driving
	12.2 Phenols
	12.3 Ethers
	12.4 Thiols
	12.5 Aldehydes and Ketones
		Structure and Physical Properties
		Nomenclature
		Important Aldehydes and Ketones
	A Medical Connection Formaldehyde and Methanol Poisoning
		Reactions Involving Aldehydes and Ketones
	A Medical Connection Alcohol Abuse and Antabuse
13 Carboxylic Acids, Esters, Amines, and Amides
	13.1 Carboxylic Acids
		Structure and Physical Properties
		Nomenclature
	Chemistry at the Crime Scene Carboxylic Acids and the Body Farm
		Some Important Carboxylic Acids
	An Environmental Perspective Garbage Bags from Potato Peels?
		Reactions Involving Carboxylic Acids
	13.2 Esters
		Structure and Physical Properties
		Nomenclature
		Reactions Involving Esters
	An Environmental Perspective The Chemistry of Flavor and Fragrance
	A Medical Connection Carboxylic Acid Derivatives of Special Interest
	13.3 Amines
		Structure and Physical Properties
		Nomenclature
		Medically Important Amines
		Reactions Involving Amines
	13.4 Amides
		Structure and Physical Properties
		Nomenclature
		Medically Important Amides
	A Medical Connection Semisynthetic Penicillins
		Reactions Involving Amides
14 Carbohydrates
	14.1 Types of Carbohydrates
	14.2 Monosaccharides
	A Medical Connection Tooth Decay and Simple Sugars
	A Medical Connection Chemistry Through the Looking Glass
	14.3 Stereoisomers and Stereochemistry
		Stereoisomers
		Rotation of Plane-Polarized Light
		The Relationship Between Molecular Structure and Optical Activity
		Fischer Projection Formulas
		The D- and L- System of Nomenclature
	14.4 Biologically Important Monosaccharides
		Glucose
		Fructose
		Galactose
		Ribose and Deoxyribose, Five-Carbon Sugars
		Reducing Sugars
	14.5 Biologically Important Disaccharides
		Maltose
		Lactose
		Sucrose
	14.6 Polysaccharides
		Starch
	Chemistry at the Crime Scene Blood Group Antigens
		Glycogen
		Cellulose
15 Lipids and Their Functions in Biochemical Systems
	15.1 Biological Functions of Lipids
	A Medical Connection Lifesaving Lipids
	15.2 Fatty Acids
		Structure and Properties
		Chemical Reactions of Fatty Acids
	Chemistry at the Crime Scene Adipocere and Mummies of Soap
		Eicosanoids: Prostaglandins, Leukotrienes, and Thromboxanes
	15.3 Glycerides
		Neutral Glycerides
		Phosphoglycerides
	15.4 Nonglyceride Lipids
		Sphingolipids
	A Medical Connection Steroids and the Treatment of Heart Disease
		Steroids
		Waxes
	15.5 Complex Lipids
	15.6 The Structure of Biological Membranes
		Fluid Mosaic Structure of Biological Membranes
		Membrane Transport
	A Medical Connection Liposome Delivery Systems
		Energy Requirements for Transport
16 Protein Structure and Enzymes
	16.1 Cellular Functions of Proteins
	16.2 The �-Amino Acids
		Structure of Amino Acids
		Stereoisomers of Amino Acids
	A Medical Connection Proteins in the Blood Classes of Amino Acids
	16.3 The Peptide Bond
	16.4 The Primary Structure of Proteins
	16.5 The Secondary Structure of Proteins
	A Lifestyle Connection The Opium Poppy and Peptides in the Brain
		a-Helix
		b-Pleated Sheet
	16.6 The Tertiary Structure of Proteins
	16.7 The Quaternary Structure of Proteins
	16.8 Myoglobin and Hemoglobin
		Myoglobin and Oxygen Storage
		Hemoglobin and Oxygen Transport
		Sickle Cell Anemia
	16.9 Denaturation of Proteins
	16.10 Enzymes
		Classification of Enzymes
		Naming of Enzymes
		The Effect of Enzymes on the Activation Energy of a Reaction
		The Enzyme-Substrate Complex
		The Transition State and Product Formation
		Cofactors and Coenzymes
		Environmental Effects
	A Medical Connection �1-Antitrypsin and Familial Emphysema
		Inhibition of Enzyme Activity
		Uses of Enzymes in Medicine
	Chemistry at the Crime Scene Enzymes, Nerve Agents, and Poisoning
17 Introduction to Molecular Genetics
	17.1 The Structure of the Nucleotide
		Nucleotide Structure
	17.2 The Structure of DNA and RNA
		DNAStructure: The Double Helix
		RNA Structure
	A Medical Connection Fooling the AIDS Virus with “Look-Alike” Nucleotides
	17.3 DNA Replication
	17.4 Information Flow in Biological Systems
		Classes of RNA Molecules
		Transcription
		Post-Transcriptional Processing of RNA
	17.5 The Genetic Code
	17.6 Protein Synthesis
		The Role of Transfer RNA
		The Process of Translation
	A Medical Connection The Ames Test for Carcinogens
	Chemistry at the Crime Scene DNA Fingerprinting
	17.7 Mutation, Ultraviolet Light, and DNA Repair
		The Nature of Mutations
		The Results of Mutations
	A Medical Connection A Genetic Approach to Familial Emphysema
		Mutagens and Carcinogens
		Ultraviolet Light Damage and DNA Repair
		Consequences of Defects in DNA Repair
18 Carbohydrate Metabolism
	18.1 ATP: The Cellular Energy Currency
	18.2 Overview of Catabolic Processes
		Stage I: Hydrolysis of Dietary Macromolecules into Small Subunits
		Stage II: Conversion of Monomers into a Form That Can Be Completely Oxidized
		Stage III: The Complete Oxidation of Nutrients and the Production of ATP
	18.3 Glycolysis
		An Overview
		Reactions of Glycolysis
	18.4 Fermentations
		Lactate Fermentation
		Alcohol Fermentation
	A Lifestyle Connection Fermentations: The Good, the Bad, and the Ugly
	18.5 The Mitochondria
		A Lifestyle Connection Exercise and Energy Metabolism
		Structure and Function
		Origin of the Mitochondria
	18.6 Conversion of Pyruvate to Acetyl CoA
	18.7 An Overview of Aerobic Respiration
	18.8 The Citric Acid Cycle (The Krebs Cycle)
		Reactions of the Citric Acid Cycle
	18.9 Oxidative Phosphorylation
		Electron Transport Systems and the Hydrogen Ion Gradient
		ATP Synthase and the Production of ATP
		Summary of the Energy Yield
	18.10 Gluconeogenesis: The Synthesis of Glucose
	18.11 Glycogen Synthesis and Degradation
		The Structure of Glycogen
A Medical Connection Diagnosing Diabetes
	Glycogenolysis: Glycogen Degradation
	Glycogenesis: Glycogen Synthesis
19 Fatty Acid and Amino Acid Metabolism
	19.1 Lipid Metabolism in Animals
		Digestion and Absorption of Dietary Triglycerides
		Lipid Storage
	19.2 Fatty Acid Degradation
		An Overview of Fatty Acid Degradation
	A Lifestyle Connection Losing Those Unwanted Pounds of Adipose Tissue
		The Reactions of �-Oxidation
	19.3 Ketone Bodies
		Ketosis
		Ketogenesis
	19.4 Fatty Acid Synthesis
		A Comparison of Fatty Acid Synthesis and Degradation
	19.5 Degradation of Amino Acids
		Removal of �-Amino Groups: Transamination
		Removal of �-Amino Groups: Oxidative Deamination
		The Fate of Amino Acid Carbon Skeletons
	19.6 The Urea Cycle
		Reactions of the Urea Cycle
	A Medical Connection Diabetes Mellitus and Ketone Bodies
	19.7 The Effects of Insulin and Glucagon on Cellular Metabolism
Glossary
Answers to Odd-Numbered Problems
Credits
Index