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John T. Moore. Biochemistry For Dummies
Biochemistry For Dummies® To view this book's Cheat Sheet, simply go to www.dummies.com and search for “Biochemistry For Dummies Cheat Sheet” in the Search box. Table of Contents
List of Tables
List of Illustrations
Guide
Pages
Introduction
About This Book
Foolish Assumptions
Icons Used in This Book
Beyond the Book
Where to Go from Here
Setting the Stage: Basic Biochemistry Concepts
Biochemistry: What You Need to Know and Why
Why Biochemistry?
What Is Biochemistry and Where Does It Take Place?
Types of Living Cells
Prokaryotes
Eukaryotes
Animal Cells and How They Work
A Brief Look at Plant Cells
Seems So Basic: Water Chemistry and pH
The Fundamentals of H2O
Let’s get wet! The physical properties of water
Water is a polar molecule
Water has strong intermolecular forces
Water has a high specific heat
Water’s most important biochemical role: The solvent
Hydrogen Ion Concentration: Acids and Bases
Achieving equilibrium
Understanding the pH scale
Calculating pOH
Applying the Brønsted-Lowry theory
Swapping hydrogens between acids and bases
Acting as either an acid or a base
Buffers and pH Control
Identifying common physiological buffers
Calculating a buffer’s pH
Fun with Carbon: Organic Chemistry
The Role of Carbon in the Study of Life
It’s All in the Numbers: Carbon Bonds
When Forces Attract: Bond Strengths
Everybody has ‘em: Intermolecular forces
London dispersion forces
Dipole-dipole forces
Hydrogen bonding
Ionic interactions
Water-related interactions: Both the lovers and the haters
How bond strengths affect physical properties of substances
Melting points, boiling points, and solubility
Odors
Getting a Reaction out of a Molecule: Functional Groups
Hydrocarbons
Functional groups with oxygen and sulfur
Functional groups containing nitrogen
Functional groups containing phosphorus
Reactions of functional groups
Alcohols
Aldehydes and ketones
Carboxylic acids
Thiols and amines
Phosphoric acid
pH and functional groups
Same Content, Different Structure: Isomerism
Cis-trans isomers
Chiral carbons
Identifying chiral molecules
Determining the chiral form: Enantiomer or stereoisomer?
Illustrating the chiral compound: Fischer projection formulas
The Meat of Biochemistry: Proteins
Amino Acids: The Building Blocks of Protein
General Properties of Amino Acids
Amino acids are positive and negative: The zwitterion formation
Protonated? pH and the isoelectric point
Asymmetry: Chiral amino acids
The Magic 20 Amino Acids
Nonpolar (hydrophobic) and uncharged amino acids
DRAWING THE STRUCTURES OF AMINO ACIDS
Polar (hydrophilic) and uncharged amino acids
Acidic amino acids
Basic amino acids
Lest We Forget: Rarer Amino Acids
Rudiments of Amino Acid Interactions
Intermolecular forces: How an amino acid interacts with other molecules
Altering interactions by changing the pH
Combining Amino Acids: How It Works
The peptide bond and the dipeptide
Tripeptide: Adding an amino acid to a dipeptide
Protein Structure and Function
Proteins: Not Just for Dinner
Primary Structure: The Structure Level All Proteins Have
Building a protein: Outlining the process
Organizing the amino acids
Example: The primary structure of insulin
Secondary Structure: A Structure Level Most Proteins Have
The -helix
The -pleated sheet
-turns and the -loops
Tertiary Structure: A Structure Level Many Proteins Have
Quaternary Structure: A Structure Level Some Proteins Have
Dissecting a Protein for Study
Separating proteins within a cell and purifying them
Separating proteins by size
FORENSICS: ANALYSIS OF BLOODSTAINS
Separating proteins by charge
Digging into the details: Uncovering a protein’s amino acid sequence
Step 1: Separating and purifying the polypeptide chains
Step 2: Slashing intrachain disulfide linkages
Step 3: Determining amino acid concentration of the chain
Step 4: Identifying the terminal amino acids
Steps 5 and 6: Breaking the chain into smaller pieces
BASICS OF BLOOD TYPING
Step 7: Combining information to get the total sequence
Step 8: Locating the disulfide linkages
Enzyme Kinetics: Getting There Faster
Enzyme Classification: The Best Catalyst for the Job
Up one, down one: Oxidoreductases
You don’t belong here: Transferases
Water does it again: Hydrolases
Taking it apart: Lyases
Shuffling the deck: Isomerases
Putting it together: Ligases
Enzymes as Catalysts: When Fast Is Not Fast Enough
All about Kinetics
Enzyme assays: Fixed time and kinetics
Rate determination: How fast is fast?
ENZYMES IN MEDICAL DIAGNOSIS AND TREATMENT
Measuring Enzyme Behavior: The Michaelis-Menten Equation
Ideal applications
Realistic applications
Here we go again: Lineweaver-Burk plots
Graphing kinetics data
Enzyme Inhibition: Slowing It Down
Competitive inhibition
Noncompetitive inhibition
Graphing inhibition
Enzyme Regulation
WHERE THE MONEY IS: ENZYMES AND INDUSTRY
Carbohydrates, Lipids, Nucleic Acids, and More, Oh My!
What We Crave: Carbohydrates
Properties of Carbohydrates
They contain one or more chiral carbons
They have multiple chiral centers
A Sweet Topic: Monosaccharides
The most stable monosaccharide structures: Pyranose and furanose forms
Chemical properties of monosaccharides
CARBON ATOM POP QUIZ
Derivatives of monosaccharides
The most common monosaccharides
The beginning of life: Ribose and deoxyribose
Sugars Joining Hands: Oligosaccharides
Keeping it simple: Disaccharides
Starch and cellulose: Polysaccharides
Bread, pasta, and potatoes: Starches
Keeping the termites happy: Cellulose
Biological connective tissue: Acidic polysaccharides
Glycoproteins
The Aldose Family of Sugars
Lipids and Membranes
Lovely Lipids: An Overview
Behavior of lipids
Fatty acids in lipids
A Fatty Subject: Triglycerides
Properties and structures of fats
Cleaning up: Breaking down a triglyceride
No Simpletons Here: Complex Lipids
Phosphoglycerides
Plasmalogens
Phosphatidates
Phosphatidylethanolamines
Phosphatidylcholines
Other phospholipids
Sphingolipids
Glycosphingolipids and cerebrosides
Gangliosides
Sphingophospholipids
Membranes: The Bipolar and the Bilayer
Crossing the wall: Membrane transport
Pumps
Channels
WHEN IS A SOLID A LIQUID? THE FLUID MOSAIC MODEL
Steroids: Pumping up
Prostaglandins, Thromboxanes, and Leukotrienes: Mopping Up
Nucleic Acids and the Code of Life
Nucleotides: The Guts of DNA and RNA
Reservoir of genetic info: Nitrogen bases
The sweet side of life: The sugars
The sour side of life: Phosphoric acid
Tracing the Process: From Nucleoside to Nucleotide to Nucleic Acid
First reaction: Nitrogen base + 5-carbon sugar = nucleoside
Second reaction: Phosphoric acid + nucleoside = nucleotide
Third reaction: Nucleotide becomes nucleic acid
A Primer on Nucleic Acids
DNA and RNA in the grand scheme of life
Nucleic acid structure
Vitamins: Both Simple and Complex
More than One-a-Day: Basics of Vitamins
To B or Not to B: B Complex Vitamins
Vitamin B1 (thiamine)
Vitamin B2 (riboflavin)
Vitamin B3 (niacin)
Vitamin B6 (pyridoxine)
Biotin
Folic acid
Pantothenic acid
The wonders of vitamin B12
Vitamin A
Vitamin C
Vitamin D
Vitamin E
Vitamin K
Hormones: The Body’s Messengers
Structures of Some Key Hormones
Proteins
Steroids
Amines
Now and Later: Prohormones
Proinsulin
ANGIOTENSIN AND ALDOSTERONE’S EFFECTS ON BLOOD PRESSURE
Angiotensinogen
Fight or Flight: Hormone Function
Opening the letter: Hormonal action
Simple control loops
Hypothalamus-pituitary control
Models of hormonal action
The second-messenger model: Like the mail
AMPLIFICATION
Steroid hormonal action
Bioenergetics and Pathways
Life and Energy
ATP: The Energy Pony Express
ATP and free energy
ATP as an energy transporter
It’s Relative: Molecules Related to ATP
The nucleoside triphosphate family
As easy as 1, 2, 3: AMP, ADP, and ATP
Where It All Comes From
WHAT HAPPENS IF YOU STOP EATING?
ATP: The Body’s Monetary System
Metabolism I: Glycolysis
Glycolysis: Phase I
Glycolysis: Phase II
Releasing the power: Energy efficiency
Going in reverse: Gluconeogenesis
Alcoholic fermentation: We’ll drink to that
Metabolism II: Citric Acid (Krebs) Cycle
Let’s get started: Synthesis of acetyl-CoA
Three’s a crowd: Tricarboxylic acids
Oxidative decarboxylation
Production of succinate and GTP
Oxaloacetate regeneration
Amino acids as energy sources
Electron Transport and Oxidative Phosphorylation
The electron transport system
Off on a tangent: Dealing with reduction potentials
Pyridine-linked dehydrogenases
Flavin-linked dehydrogenases
Iron-sulfur proteins
Ubiquinones
Cytochromes
Interpersonal relationships (No, it’s not what you think)
Oxidative phosphorylation
Proposed mechanisms
ATP production
Involving the fats: β-oxidation cycle
Not so heavenly bodies: Ketone bodies
THE OTHER GUY
Investing in the Future: Biosynthesis
Fatty acids
Membrane lipids
Amino acids
Smelly Biochemistry: Nitrogen in Biological Systems
Ring in the Nitrogen: Purine
Biosynthesis of purine
Inosine synthesis
AMP synthesis
GMP synthesis
How much will it cost?
Pyrimidine Synthesis
First step: Carbamoyl phosphate
Next step: Orotate
Last step: Cytidine
Back to the Beginning: Catabolism
Nucleotide catabolism
Amino acid catabolism
Heme catabolism
Process of Elimination: The Urea Cycle
Amino Acids Once Again
Metabolic Disorders
Gout
Lesch-Nyhan syndrome
Albinism
Alkaptonuria
Phenylketonuria
Genetics: Why We Are What We Are
Photocopying DNA
Let’s Do It Again: Replication
DNA polymerases
The current model of DNA replication
Mechanisms of DNA repair
TELOMERES AND AGING
Direct repair
Base-excision repair
Nucleotide-excision repair
Mutation: The good, the bad, and the ugly
Restriction enzymes
Mendel Rolling Over: Recombinant DNA
Patterns: Determining DNA Sequences
Getting charged up about gel electrophoresis
Determining the base sequence
The butler did it: Forensic applications
Methods of analysis
Paternity testing
Genetic Diseases and Other DNA Testing Applications
GENETIC TESTING IN SPORTS
Sickle cell anemia
Hemochromatosis
Cystic fibrosis
Hemophilia
ETHICS OF GENETIC MODIFICATION AND TESTING
Tay-Sachs disease
Transcribe This! RNA Transcription
Types of RNA
mRNA AND THE CREATION OF A VACCINE FOR COVID-19
RNA Polymerase Requirements
Making RNA: The Basics
Promoting transcription of RNA
Prokaryotic cells
Eukaryotic cells
Not a Secret Any Longer: The Genetic Code
Codons
Alpha and omega
Models of Gene Regulation
The Jacob-Monod (operon) model
The lac operon
Other prokaryotic regulators
Regulation of eukaryotic genes
Histones
Mediating transcription
Translation: Protein Synthesis
Hopefully Not Lost in Translation
Who needs translation, anyway?
Home, home in the ribosome
The Translation Team
The team captain: rRNA
Here’s the snap: mRNA
Carrying the ball: tRNA
Charging up the middle: Amino acid activation
Hooking Up: Protein Synthesis
Activation
Initiation
Elongation
Termination
The wobble hypothesis
Variation in Eukaryotic Cells
Ribosomes
THE HUMAN GENOME PROJECT
Initiator-tRNA
Initiation
Elongation and termination
The Part of Tens
Ten Great Applications of Biochemistry
Ames Test
Pregnancy Testing
HIV Testing
Breast Cancer Testing
Prenatal Genetic Testing
PKU Screening
Genetically Modified Foods
Genetic Engineering
Cloning
Gene-Replacement Therapy
Ten Biochemistry Careers
Research Assistant
Nanotechnologist
Quality Control Analyst
Clinical Research Associate
Technical Writer
Biochemical Development Engineer
Forensic Scientist
Patent Attorney
Pharmaceutical Sales Representative
Biostatistician
Index. Symbols
Numbers
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
About the Authors
Dedication
Authors’ Acknowledgments
WILEY END USER LICENSE AGREEMENT
