The Bacteria: Their Origin, Structure, Function and Antibiosis

✍ Scribed by Arthur L. Koch

• Tongue: English
• Leaves: 216
• Category: Library

✦ Synopsis

Understanding antibiotic chemotherapy at the ecological level is necessary for more permanent advances in development and in the usage of antibiotic agents. This book traces the history of bacteria, from the development of life on earth to the evolution of diversity. It is this diversity that led, almost automatically to the development of pathogens as well as antibiotics. If we are to create long term antibiotics we must design them with this history in mind.

✦ Table of Contents

Table of Contents
Preface
Legend to the Frontispiece: The Structural Elements of the Bacterial Wall: Five Disaccharide Penta-muropeptides Forming a Glycan Chain and Two about to Form a Nona-muropeptide
Part 1 Origin of Bacteria
Chapter 1 The Origin of Life Based on Physical Principles
THOUGHTS ABOUT THE ORIGIN OF LIFE
ASTROBIOLOGY
THREE LAWS OF THERMODYNAMICS
CHEMICAL REACTIONS
THE MECHANICS OF COVALENT BONDING
REARRANGING COVALENT BONDS
CATALYZED REACTIONS
DRIVING A CHEMICAL REACTION
Chapter 2 Preamble to Life
THE ABIOTIC WORLD
RESOURCES AVAILABLE FOR LIFE
THE STAGES OF DEVELOPMENT OF LIFE
THE GENERATION AND PRODUCTION OF THE ORGANIC MOLECULES NEEDED FOR LIFE
Chapter 3 The First Cell
ENERGY TRANSDUCTION FOR BIO-UTILIZATION
THE REPLICATION OF MACROMOLECULES
THE FIRST CELL DEPENDED ON ABIOTICALLY FORMED BUT SELECTIVE CATALYSTS
THE THREE MOST ESSENTIAL PROCESSES CARRIED OUT BY THE FIRST CELL
Chapter 4 Development of Cell Physiology and Diversity
CLASSES OF METABOLIC SYSTEMS THAT HAVE DEVELOPED IN THE LIVING WORLD
SEMI-CONSERVATIVE REPLICATION AND TRANSLATION
ONE MUTATION AT A TIME TO DEVELOP MANY DIFFERENT METABOLIC SYSTEMS
EVOLUTION DURING THE INTERVAL BETWEEN THE FIRST CELL AND THE LAST UNIVERSAL ANCESTOR
THE DEVELOPMENT OF CELLULAR PROCESSES DURING THE ERA OF PROGRESSIVE EVOLUTION
CONTROLLING THE REDUNDANCY OF GENETIC ELEMENTS
MEETING ENVIRONMENTAL CHALLENGES
BIOENERGY BEFORE THE LAST UNIVERSAL ANCESTOR
THE GAUSIAN PRINCIPLE AND ITS RELEVANCE
LINEAR EVOLUTION VERSUS BRANCHING EVOLUTION
MODEL FOR THE DEVELOPMENT OF DIVERSITY
Part 2 Wall Structure
Chapter 5 Covalent Bonds and Tensile Strength of Materials
STRENGTH FROM BONDING AND STRUCTURE
VISCOELASTIC PROPERTIES AND TEARING OF SOLIDS
MATERIALS WITH WET STRENGTH
WALL SYNTHESIS AND THE MAKE-BEFORE-BREAK STRATEGY
INTRODUCTION TO THERMODYNAMICS
CHEMICAL BONDS
THE THERMODYNAMICS OF BOND FORMATION
Chapter 6 Structure of the Fabric that Covers a Bacterium
THE PENTA-MUROPEPTIDE DISACCHARIDE
THE CROSS-LINKED FABRIC-LIKE STRUCTURE OF THE BACTERIAL WALL
OTHER MUREIN WALLS
ENERGY FOR WALL SYNTHESIS
WALL SYNTHESIS AND THE MAKE-BEFORE-BREAK STRATEGY
BIOSYNTHESIS OF PEPTIDOGLYCAN
VARIATION OF THE BASIC UNIT AND THE LINKAGE OF THE CROSS-BRIDGE
FORMATION OF THE DISACCHARIDE UNIT
FORMATION OF THE MUROPEPTIDE PORTION
TRANSPORT AND LINKING
Chapter 7 The Covalently Linked Sacculus: the Nona-Muropeptide Model
CONFORMATION OF THE GLYCAN STRAND
GLYCAN LENGTH DISTRIBUTION
FORMATION OF THE NONA-MUROPEPTIDE
A STRESS-CONTROLLED MODEL FOR BACTERIAL WALL GROWTH
Chapter 8 The Structure of the Tessera; the Unit Structure of MureinWall
THE TESSERA
THE UNIT OF GRAM-NEGATIVE AND GRAM-POSITIVE WALL ARCHITECTURE: THE TESSERA
THE IN VIVO SACCULUS IS NOT MAXIMALLY EXTENDED
Chapter 9 Extrusion and Incorporation into Wall
THE CHEMICAL NATURE OF THE PENTA-MUROPEPTIDE-BACTOPRENOL COMPLEX
INSERTION OF A NEW UNIT INTO A GROWING CHAIN
Chapter 10 The Role of Poles in the Growth Strategy of Bacteria
HOW DO BACTERIA KEEP FROM GROWING EVER LARGER?
AN EXPLANATION FOR INERTNESS OF THE POLES OF GRAM-POSITIVE RODS
AN EXPLANATION FOR INERTNESS OF THE POLES OF GRAM-NEGATIVE RODS
CONCLUDING REMARKS
Part 3 Bacterial Morphologies
Chapter 11 Sidewalls of Gram-Negative Rod-Shaped Bacteria
SOAP BUBBLE ANALOGY TO BACTERIAL GROWTH
STAINING OF THE OLD MUREIN
MODELS FOR SIDEWALL GROWTH
IS THERE HELICAL WALL IN E. COLI?
Chapter 12 Growth Strategies for Gram-Positive Cells
BIOPHYSICS OF WALL DEVELOPMENT
THE GRAM-POSITIVE STRATEGY FOR THE SIDEWALL OF ROD-SHAPED CELLS
THE GRAM-POSITIVE STRATEGY FOR THE POLES OF ROD-SHAPED CELLS
STRESS DISTRIBUTION IN THE THICK WALLS OF GROWING GRAM-POSITIVE ROD-SHAPED BACTERIA
AUTOLYSINS AND TURNOVER
A MECHANISM FOR A ROD-SHAPED CELL TO FIND ITS MIDDLE AND SEPARATE SEGREGATED DAUGHTER CHROMOSOMES AND CELLS
Chapter 13 Wall Growth Strategies for Gram-Negative Cells
THE GRAM-NEGATIVE WALL STRUCTURE
THICKNESS, TURNOVER, AND ELASTICITY OF MUREIN WALL
THE CONNECTIVITY OF THE SACCULAR WALL
THE NORMAL STRETCHING OF THE MUREIN FABRIC DURING BALANCED GROWTH
ESTIMATION OF THE DEGREE OF MUREIN STRESS BY STOP-FLOW TURBIDITY MEASUREMENTS
ESTIMATION OF THE DEGREE OF MUREIN STRESSING FROM MEASUREMENTS OF GROWING FILAMENTS SHRINKAGE AS THE CELLULAR MEMBRANES ARE RUPTURED
SIGNIFICANCE OF THE IN VIVO EXPANSION OF THE SACCULUS ABOVE THE RELAXED STATE
GENERATION OF THE ROD-SHAPE AND POLE DEVELOPMENT
THE PROBLEMS CAUSED BY BEING THIN-WALLED
THE CONTRAST WITH THE GRAM-POSITIVE STRATEGY
Chapter 14 Commas, Vibrios, Spirilla, and Helicobacters; Tapered and Branched Bacteria
THE RANGE OF BACTERIAL SHAPES
MODERATELY CURVED BACTERIAL RODS
POSSIBLE MODELS FOR CURVATURE
COMMAS AND VIBRIOS
SPIRILLA
HELICOBACTERS
TAPERED CELLS
KNOBS AND BRANCHES
HOW DO BACTERIA BRANCH?
GENERATION OF CORYNEBACTERIA-LIKE MORPHOLOGY IN E. COLI
THE PATCHY NATURE OF THE SIDEWALLS OF E. COLI
THE GROWTH-INHIBITORY ROLE OF POLES IN THE MAINTENANCE OF THE DIAMETER DURING ROD AND COCCAL CELL DEVELOPMENT
PENICILLIN-BINDING PROTEINS (PBPs) AND CONTROL OF WALL SYNTHESIS
THE TRANSPEPTIDASE ACTION OF LARGE AND SMALL PBPs
THE PHYSICS OF SURFACE EXPANSION WHEN THERE IS AN INERT PORTION OF THE WALL
THE INITIATION OF A BRANCH OR KNOB
HYPOTHESIS FOR THE GENERATION OF BRANCHES OR KNOBS
THE NONA-MUROPEPTIDE STRESS MODEL AND SIDEWALL GROWTH
GENERALIZATIONS
Chapter 15 Spirochetes and Spiroplasma and the Special Strategies for CWD (CellWall Deficient) Cells
SPIROCHETES
SPIROPLASMA
BACTERIAL L-FORMS AND THOSE WITH CELL DEFICIENT WALLS
THE RATIONALE FOR THE EXISTENCE OF CELL WALL DEFICIENT (CWD) ORGANISMS
THE INSECT CONNECTION
THE EVOLUTIONARY CONNECTION
INSECT OSMOTIC PRESSURE
COULD AMYOTROPHIC LATERAL SCLEROSIS BE CAUSED BY A SPIROCHETE?
Chapter 16 Coccal Versus Rod-Shaped Cells, and the First Bacterium
THE FIRST BACTERIUM RESULTED FROM THE DEVELOPMENT OF THE SACCULUS
EVOLUTION FROM THE FIRST CELL TO THE LAST UNIVERSAL ANCESTOR
WAS THE WORLD BIOLOGICALLY DIVERSE BEFORE THE LUA AROSE?
HOW DID DIVERSITY ARISE?
THE IMPORTANT ADVANTAGES OF HAVING A SACCULUS
WERE GRAM-POSITIVE ROD-SHAPED CELLS THE FIRST BACTERIA?
ARGUMENTS FOR GRAM-POSITIVE ROD-SHAPED CELLS ARISING FIRST
ARGUMENTS FOR GRAM-NEGATIVE CELLS ARISING FIRST
WAS THE FIRST BACTERIUM COCCUS OR ROD?
WALL GROWTH MECHANISMS FOR THE FIRST BACTERIUM
CONCLUSION ABOUT BACTERIAL ORIGINS
Chapter 17 Diseases: Old and New
INTRODUCTION
THE ADVANTAGE OF BEING STD IN A SPARSELY POPULATED WORLD
DISEASES IN PRIMITIVE HUMANS
THE SIMILARITY OF THE STRATEGY OF THE CAVE MAN’S DISEASES AND THE MODERN PRIMATE PATHOGENS
SELECTION FOR “GENTLE” RETROVIRUSES AND THE MUCOSAL IMMUNE SYSTEM
SECRETORY LEUKOCYTE PROTEASE INHIBITOR
VARIABLE STIMULATION OF THE IMMUNE SYSTEM OF PRIMATES UNDER DIFFERENT CONDITIONS
EPIDEMIOLOGY OF AIDS AND THE “RAPID” CHANGE OF HIV
WHY THE MAMMALIAN STD PATHOGENS MUST PROTECT THE HOST’S NEWBORN FROM THEIR OWN LETHAL ACTION
THE COPING STRATEGIES OF HIV, HTLV-I, AND HTLV-II
HOW HIV IS “GENTLE” TO ITS HOST
SOME GENERAL CONCLUSIONS ABOUT HOST-PARASITE RELATIONS
Part 4 Antibiosis
Chapter 18 Lysozymes as Alternatives to ß-lactams Antibiotics Acting on the Bacterial Wall
THE ß-LACTAMS
THE LYSOZYMES
THE FUTURE
Chapter 19 Development of Wall Antibiotics and Bacterial Counter-Measures
PRODUCTION OF ß-LACTAMS AND SUBSEQUENT PRODUCTION OF ß-LACTAMASES
ß-LACTAMS
ß-LACTAMASES
RESISTANCE MECHANISMS IN GENERAL; DEVELOPMENT OF ß-LACTAMASES IN PARTICULAR
LACTAMASE-RESISTANT LACTAMS EXTANT BEFORE MEDICINAL CHEMISTRY
OVERVIEW OF EARLY ß-LACTAM EVOLUTION
TURGOR PRESSURE RESPONSES TO WALL ANTIBIOTICS
MRSA (METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS)
LACTAM ANTIBIOTICS TODAY
ß-LACTAMASES DESTROYING ß-LACTAMS IN THE CURRENT ANTIBIOTIC ERA
INITIAL MANUFACTURE OF PENICILLINS AND THE MICROBIOLOGICAL SEQUELAE
NOVEL ß-LACTAMS
EXTENDED-SPECTRUM BETA LACTAMASES (ESBL) AND CEPHALOSPORINASES
WHAT ABOUT THE FUTURE
Chapter 20 Antibiotics and Resistance, with an Emphasis on Aminoglycosides
ANTIBIOTIC RESISTANCE MECHANISMS
ANTIBIOTIC RESISTANCE EVOLUTION WITH AND WITHOUT MAN’S INTERFERENCE
SLOW, LABORIOUS EVOLUTION OF NEW DE NOVO PROTEINS
LACK OF EVOLUTION OF NOVEL ANTIBIOTIC RESISTANCE AFTER MASSIVE HUMAN USE OF ANTIBIOTICS
ROLE OF TRANSFORMATION, PLASMIDS AND VIRUSES
SMALL BUT IMPORTANT CHANGES IN THE CURRENT ANTIBIOTIC ERA
THE EARLIEST RESISTANT MECHANISM, A VERY SPECIAL CASE
THE LATER CONTEMPORARY HISTORY OF AMINOGLYCOSIDES
Chapter 21 Future Chemotherapy Aimed at the Bacterial Murein
ANTIBIOTIC RESISTANCE MECHANISMS
EVOLUTION OF ANTIBIOTIC RESISTANCE WITH AND WITHOUT MANKIND’S INTERFERENCE
SLOW, LABORIOUS EVOLUTION OF NEW PROTEINS
LACK OF EVOLUTION OF NOVEL ANTIBIOTIC RESISTANCE AFTER MASSIVE HUMAN USE OF ANTIBIOTICS
ROLE OF TRANSFORMATION, PLASMIDS AND VIRUSES
ANTIBIOSIS AND COUNTER-MEASURES OF THE ANTIBIOTIC ERA
LACTAM ANTIBIOTICS AND VARIANTS TODAY
EXTENDED-SPECTRUM BETA LACTAMASES (ESBL) AND CEPHALOSPORINASES
WHAT TO DO AND WHERE TO LOOK
THE END GAME
References