1. Miller tried to reconstruct primitive conditions by passing electrical sparks through a mixture similar to the hypothetical primitive atmosphere.

2. Miller found that after several days, the mixture in the apparatus had formed quite a variety of organic compounds, including the common amino acids.

3. Miller's experiment has been repeated many times with various initial mixtures, always with similar results.

1. Fox and his colleagues later found that hot, salty solutions of peptides form microspheres as they cool.

2. Microspheres are stable nonliving structures with many properties of modern procaryotic cells and about the same size (about 2 µm in diameter).

1. Further evolution requires that metabolism be confined to small, enclosed spaces where high concentrations of metabolites and enzymes can develop.

2. Genetic systems must be confined to cells to take advantage of mutational novelties; evolution depends on competition among individuals (cells or organisms), and this could not happen if each genetic novelty were shared with a large system.

1. RNA molecules have an inherent ability to interact with one another through base-pairing, so they can replicate as DNA does.

2. RNA molecules can also fold into complicated forms and act as ribozymes which are RNA molecules that catalyze chemical reactions just as protein enzymes do.

3. During the RNA-world stage of evolution, many of the functions now performed by proteins must have been performed by RNA molecules.

1. Some RNAs had the potential to become genomes ("protogenomes") because their base sequences allowed them to replicate with particular ease.

2. Other RNAs, having an affinity for specific amino acids, then served as primitive transfer RNAs by helping to line up amino acids along a protogenome, thus catalyzing a simple protein synthesis.

1. These cells must have evolved pathways for mobilizing energy through fermentation, probably including the glycolytic pathway, producing ATP by substrate-level phosphorylation, with no electron transport system.

2. Suppose, at this early stage of evolution, a critical monomer became depleted. Only the organisms that had an enzyme for converting another compound into the one that was depleted survived.

3. Through mutation and natural selection, pathways for biosynthesis evolved, and organisms gradually became more independent (Figure 29.4).

1. Plant photosynthesis, which produces oxygen as a byproduct (oxygenic photosynthesis), is an advanced form that requires two photosystems and must have taken a long time to evolve.

2. Around 2.0—1.8 billion years ago, phototrophs probably used various forms of anoxygenic photosynthesis, which does not produce oxygen as a byproduct.

3. The first phototrophs probably used a form of photosystem I just to oxidize organic substrates. This text refers to these organisms as stage 1.

4. The modern survivors of that retain stage-1 photosynthesis are green sulfur bacteria and purple non-sulfur bacteria (Figure 29.5).

5. Stage-2 photosynthesis came about with the evolution of the PCR (Calvin—Benson) cycle.

6. Modern purple sulfur bacteria use stage-2 photosynthesis and can only grow anaerobically in the light using H2S as an electron donor instead of H2O (Figure 29.6).

7. With the development of photosystem II, oxygenic photosynthesis finally evolved (stage 3).

8. Stage-3 photosynthesis is used in modern cyanobacteria (blue-green bacteria; Figure 29.7).

9. Cyanobacteria have the same chlorophyll a as eucaryotic phototrophs, and they produce oxygen as a byproduct of photosynthesis.

1. Oxygenic photosynthesis began to shift the atmosphere from reducing to oxidizing.

2. The evolution of cytochrome enzymes that could reduce oxygen to water was a great event that created modern aerobic respiration.

3. Since the DNA genome is vulnerable to destruction by oxygen, it was advantageous to sequester it in a nucleus and to confine oxygen utilization and production to separate organelles, to mitochondria and chloroplasts.

4. When cells evolved mitochondria and chloroplasts, they could become larger, with local regions of the cytoplasm served by these ATP factories.

1. Most procaryotes are single cells with diameters on the order of 1 µm or less.

2. Some procaryotes are as large as 10—30 µm in diameter and one recently-discovered bacteria has cell lengths of about 300 µm (Figure 29.9).

1. Each procaryotic cell bears a single chromosome, usually circular.

1. Bacterial cell walls are made of a murein, or peptidoglycan, which is a polymer made by bonding two kinds of monomers into a two-dimensional network (Figure 29.10).

2. Mureins are the largest covalently bonded molecules in the world.

3. Bacterial cell walls are often rigid but porous, and they give bacteria their characteristic shapes.

1. Bacteria can be a general term used for all procaryotes, but it is not very descriptive.

2. Bacteria often exist in the form of rods, spirals (spirilla, singular spirillum) and curved cells, and spheres (cocci, singular coccus) (Figure 29.11).

3. The shapes of the bacteria often provide both the formal and informal names of bacteria such as diplococci (pairs of cocci), streptococci (chains of cocci), and staphylococci (random clumps of cocci).

1. Spirochetes propel themselves by contracting an axial filament made of fibers similar to bacterial flagella.

2. Some spirochetes are 500 µm long, yet they are thin enough (0.1—0.6 µm in diameter) to pass through filters that remove most bacteria.

3. Most spirochetes are soil and water organisms.

4. Some spirochetes are pathogens, such as Treponema pallidum, the causative agent of syphilis.

1. Slime bacteria move with a gliding mechanism and are common in soils, on rotting materials and in animal dung (Figure 29.13).

2. Myxobacteria aggregate into mushroom-like clusters, which sometimes become quite large.

3. Stalked bacteria (Figure 29.14) are common in contaminated water.

1. Mycobacteria cells are irregular and branched with unusual cell walls containing complex lipids.

2. Actinomycetes, which are closely related to mycobacteria, form long, branched, filaments with many nucleoids, but they are coenocytic because they lack cross-walls or have only incomplete walls (Figure 29.15).

3. Streptomyces, a representative actinomycete, reproduces by forming spores, each containing a chromosome, at the end of each filament.

1. Mycoplasmas lack cell walls and can grow into irregular elongated forms.

2. Mycoplasmas contain the minimal apparatus needed for metabolism and reproduction.

3. Some mycoplasmas are harmless while others are the agents of plant and animal diseases such as pleuropneumonia, a lung infection of cattle.

1. The first criterion is cell morphology.

2. The second criterion is metabolic pattern (Figure 29.17).

3. The third criterion for classifying bacteria is their reaction to the Gram stain (Figures 29.19 and 29.20).

1. An organism's way of life is obligate if it is obliged to live a certain way with no other options.

2. An organism's way of life is facultative if it can live one or more different ways.

3. Obligate anaerobes, for instance, can only live in environments with no trace of oxygen, while facultative anaerobes can survive either with or without oxygen (Figure 29.18).

1. Bacteria (and molds) produce extracellular hydrolytic enzymes that attack the polymers of these wastes, releasing monomers on which they, and others that share their living space, can grow.

2. Bacteria in turn become food for small animals, and thus some of their mass is recycled back into the food chain.

1. Sometimes two or more species of bacteria cooperate fortuitously to degrade an unusual organic compound step-wise by combining their enzymatic capabilities, although each one by itself is unable to grow on the compound.

2. Figure 29.21 shows a simple cycle between a phototrophic bacterium and a sulfate-reducing bacterium.

3. Figure 29.22 shows a similar cycle between a chemoautotroph that reduces CO2 to organic compounds and a nitrogen fixer that produces nitrogenous compounds.

4. Through this kind of mutualism, the two organisms grow together much better than either could grow alone.

1. Functional disease, such as heart disease, results from a malfunction in the organism itself.

2. Infectious disease, is due to some other organism or virus that grows as a parasite, obtaining its nourishment on the surface of the host (ectoparasitism) or somewhere within its intestinal tract or other cavities, or even within its tissues (endoparasitism).

3. Diseases are caused by bacteria, protozoans, fungi, worms, and viruses.

4. Some small bacteria can even grow inside larger bacteria (Figure 29.23).

1. In 1835, Charles Cagniard-Latour and Theodor Schwann showed independently that fermentation in beer and wine is caused by the growth of a microorganism, yeast.

2. Chemists of the day found the Cagniard-Latour/Schwann findings to be totally ridiculous. The chemists believed that fermentation was a purely chemical process.

3. Pasteur showed that by transferring yeasts and bacteria from one culture to another, would transfer the fermentative activity.

4. Pasteur also showed that when wines become sour it is because they are contaminated with undesirable bacteria.

5. In order to counter such contamination, Pasteur invented the process now called pasteurization, in which the wine (or other food such as milk) is heated briefly, just enough to kill the responsible organisms while leaving the food unharmed.

1. In the 1860s, he demonstrated the infectious agents were indeed responsible for silkworm diseases, which at the time were ravaging the French silk industry.

2. In the 1870s, Pasteur and Robert Koch showed that bacteria were causing anthrax, a disease that can strike many mammals, including humans.

3. Koch found that anthrax bacteria form protective spores that may endure for a long time, so animals may be infected merely by grazing in certain pastures.

1. The organism must be recovered from animals that have the disease.

2. The organism must be grown in pure culture.

3. When healthy animals are inoculated with this culture, they must contract the disease.

4. The organism must again be recoverable from an inoculated animal.

1. Clostridium perfringens is an extremely invasive pathogen that causes gas gangrene. Clostridia form spores that may lie dormant in the soil for a long time until they are carried into a wound, especially a deep puncture wound. If untreated, the cell- and tissue-destroying bacteria thrives leaving decaying tissue behind.

2. Clostridium botulinum, the agent of botulism, produces the botulinus toxin that paralyzes the neuromuscular junctions where nerve endings contact muscles.

1. Most organisms achieve an equilibrium with one another, so the hangers-on do the larger organisms no particular harm (commensalism) and may even help it (mutualism).

2. The human mouth has a plentiful and varied flora which may include many types of bacteria and even fungi (Figure 29.24).

1. Most of the organisms that live in these areas are generally harmless and some are even essential and beneficial.

2. Some bacteria occupy spaces that pathogens might otherwise occupy and their acid byproducts inhibit the growth of other organisms.

3. Every organism living in or on another is potentially an opportunist, and if the occasion arises for a microorganism to grow faster at the expense of its host, it will do so.

4. E. coli is an example of bacteria that normally lives in the human intestinal tract. If this bacteria makes its way into the human urogenital system, it can cause infection that must be treated.

1. The reservoir of infection for human disease may be in other people, in other animals, or in the soil.

2. The agent may be transmitted to the host by direct contact, through contaminated objects or food, via airborne particles, from infected large animals, and by insects or other invertebrate vectors.

3. Vectors are animals that can transmit pathogens from one host to another.

4. Rabies is a virus that can be transmitted from mammals and birds to humans via bite wounds.

1. The Y. pestis reservoir is primarily wild rodents, although several other kinds of mammals may be infected.

2. The Y. pestis vector is primarily rat fleas.

3. The disease known as plague devastated human populations several times in recorded history.

4. The disease can now be easily controlled with modern antibiotic therapy.

1. Malaria protozoa and yellow-fever viruses are transmitted by mosquitoes, African sleeping sickness protozoa by the tsetse fly.

2. Each pathogen has a reservoir among humans, other mammals, or birds, and it uses the arthropod as a vector.

1. Plant pathogens may have a difficult time penetrating the tough, waxy walls of their hosts.

2. Nematode worms, which open holes in the plant epidermis, are notorious vectors for plant pathogens.

1. The rickettsias are named for their discoverer, Howard T. Ricketts, who died in Mexico in 1910 from typhus fever, a rickettsial disease he was studying (Figure 29.26).

2. The rickettsias are true bacterial cells, typically about 0.3 by 1.0 µm.

3. They are intracellular parasites that can only reproduce within a host cell because they lack certain metabolic machinery.

4. Usually they infect cells of arthropods which transmit them to humans and other animals through bites.

1. Chlamydias are unable to metabolize glucose to make their own ATP.

2. Chlamydias are responsible for the eye infection trachoma, a frequent cause of blindness.

3. Chlamydias are also responsible for lymphogranuloma venereum, one of the lesser-known sexually transmitted diseases of humans.

1. Microorganisms that produce ethanol provide a substrate for others that produce vinegar.

2. Wine must be kept anaerobic to prevent the growth of bacteria such as Acetobacter, which converts the ethanol into acetic acid.

1. One ancient solution was salting and smoking which produces meats such as ham, bacon, and salt herring.

2. Sauerkraut and cucumbers were pickled, a preservation technique that relies on the action of lactate-producing bacteria.

3. Lactate-producing bacteria have long been used to convert milk into buttermilk, yogurt, and cheeses.

a. Andre Lwoff, a French virologist, observed that viruses differ from organisms in several significant ways.

a. The nucleic acid and capsid of a virion form a nucleocapsid (Figure 29.28).

b. A protective capsid can be assembled around a nucleic acid to make either a helical or a spherical structure.

a. Viruses have varied modes of infection.

b. Eventually, the infected cell falls apart and liberates many virions that have accumulated within.

a. Viruses are classified on the basis of several factors.

b. Deoxyviruses have DNA genomes.

c. Riboviruses are those with RNA genomes.

d. Interactions between viruses and their hosts run the gamut from the most virulent to the most benign.

e. Among viruses that attack humans, a wide range of symptoms and levels of severity are demonstrated.

a. A few plant diseases have been traced to particles called viroids that are even simpler than viruses.