Table of Contents
Table of Contents
Preface
About the Authors
Study Aids
Section I. Microbial Activity
1. The World of Microbes
· Introduction
· What is a microbe?
· Having a long past
· Being small
· Being many
· Growing and persisting
· Colonizing every niche and making Earth inhabitable
· Shaping the planet
· Making a living
· Cooperating for complex endeavors
· Conclusions
· Study questions
Section II. Structure and Function
2. Prokaryotic Cell Structure and Function: Envelopes and Appendages
· Prokaryotic cells
· Microscopes
o Newer microscopes
§ Scanned-proximity probe microscopes
§ Molecular stains
· Prokaryotes have complex envelopes and appendages
· The cell membrane
· How the cell membrane is protected
o The gram-positive solution
o The gram-negative solution
o The acid-fast solution
o Crystalline surface layers
o Bacteria without cell walls: the mycoplasmas
o Cell envelopes of the Archaea
· Capsules, flagella, and pili: how prokaryotes cope in certain environments
o Capsules and slime layers
o Flagella
o Pili
· Study questions
3. Prokaryotic Cell Structure and Function: the Cell Interior
· General observations
· The nucleoid
· The cytoplasm
· Inclusions and vesicles
o Gas vesicles
o Organelles for photosynthesis and chemosynthesis
o Carboxysomes
o Enterosomes
o Storage granules and others
· Conclusions
· Study questions
Section III. Growth
4. Growth of Microbial Populations
· Introduction
· How to measure growth of a bacterial culture
· When should the growth rate be determined?
· The law of growth
· Balanced growth
· Continuous culture
· How is the physiology of the cells affected by the growth rate?
· Effects of temperature, hydrostatic pressure, osmotic strength, and pH
o Temperature
§ Effect on growth rate
§ Classifying the temperature responses of microbes
§ Growth limits at temperature extremes
§ Lethal effects
o Hydrostatic pressure
o Osmotic pressure
o pH
· Conclusions
· Study questions
5. Making a Cell
· Introduction
· Growth metabolism: making life from nonlife
· Framework of growth metabolism
o Making two from one
o Assembling cell structures
o Making macromolecules
o Synthesizing building blocks
o Fueling
· Global effects of growth metabolism
o Earth’s chemical cycles
o Bioremediation
· Summary and plan
· Study questions
6. Fueling
· Overview of fueling reactions
· Getting energy and reducing power
o Driving force and its generation
o Substrate level phosphorylation and fermentation
o Transmembrane ion gradients
§ Respiration
§ Photosynthesis
§ Enzyme pumps
§ Scalar reactions
o Oxygen and life
· Making precursor metabolites: heterotrophy
o Acquiring nutrients
§ Transport through the OM of gram-negative bacteria
§ Transport through the cell membrane
o Feeder pathways
o Central metabolism
§ Common pathways of central metabolism
§ Auxiliary pathways of central metabolism
§ Diversity and flexibility of central metabolism
· Making precursor metabolites: autotrophy
o The Calvin cycle
o Other CO2-fixing cycles
· Summary
· Study questions
7. Biosynthesis
· Some general observations
o Biosynthesis and nutrition
o Bacterial studies and biosynthetic pathways
o The concept of a biosynthetic pathway
· Assimilation of nitrogen
o Central actors: glutamate and glutamine
o Synthesis of glutamate and glutamine
o Getting ammonia
o Ammonia from dinitrogen
· Assimilation of sulfur
· Assimilation of phosphorus
· Pathways to building blocks
o Amino acids
o Nucleotides
o Sugars and sugar-like derivatives
o Fatty acids and lipids
· Summary
· Study questions
8. Building Macromolecules
· Introduction
· DNA
o Overview of replication
o Initiation of replication
o DNA strand elongation
o Repair of errors in replication
o Termination of replication
o Protecting the DNA
o Assembly of the nucleoid
· RNA
