Microbe

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