The Origin and Evolution of Microbial Life: Prokaryotes and Protists - Chapter 16

AP Biology CMR @CHS ‘95 B.Rife page 1 / 9

V. Unit 5: The Origin and Evolution of Microbial Life: Prokaryotes and Protists - Chapter 16 I. Introduction A. The evolution of life has had a profound effect on the Earth. 1. Photosynthetic cyanobacteria evolved very early in the history of life and left unique fossilized communities as stromatolites. 2. Modern-day cyanobacteria of this type, less common because of predation, are virtually indistinguishable from the early forms. 3. In addition to being the ancestors of today’s cyanobacteria, these first cyanobacteria produced the Earth’s first oxygen-rich atmosphere.

B. This chapter begins a survey of all Earth’s life forms (zoology) in an evolutionary context, beginning with the very big steps of the evolution of life itself. The earliest organisms were ancestors of modern prokaryotes. They and the first eukaryotes (early protists) have inhabited our planet for a much longer time than members of any other kingdom.

C. Life began on a young Earth (16.1) 1. The age of the universe is estimated to be between 10 and 20 billion years old, while Earth coalesced from gathering interstellar matter about 4.6 billion years ago (bya). 2. Volcanic gases released water vapor, carbon monoxide, carbon dioxide, nitrogen, methane, and ammonia into the early atmosphere. 3. Earth’s crust cooled and solidified about 4.1 bya, condensing water vapor into early seas. 4. Fossil evidence shows early cyanobacteria by 3.5 bya (oldest rocks). 5. Because cyanobacterial photosynthesis is complex and advanced, the first cells likely evolved earlier, perhaps as early as 4.0 bya.

II. How did life originate (16.2) A. Some early writers believed life arose by spontaneous generation. 1. Experiments in the 1600s showed that larger organisms cannot arise spontaneously from nonliving matter.. 2. In the 1860s, French scientist Louis Pasteur confirmed that all life today, including microbes, arises only from preexisting life.

B. Most biologists subscribe to the hypothesis that the earliest life forms were simpler than any that exist today, and that they evolved from nonliving matter. 1. Although extraterrestrial organic molecules could have seeded Earth’s early environment, most scientists think these molecules arose from nonorganic molecules present in the early oceans and atmosphere. AP Biology CMR @CHS ‘95 B.Rife page 2 / 9

2. A possible scenario: Monomers evolve first, then polymers, then aggregates that eventually formed in the particular arrangement that allowed simple metabolism and self-replication. Data supporting the likelihood of many of these steps exist from a number of experiments.

C. Talking About Science: Stanley Miller’s experiments showed that organic molecules could have arisen on a lifeless Earth (16.3) 1. In the 1920s, Russian biochemist A.I. Oparin and English geneticist B.S. Haldane proposed that organic chemistry could have evolved in the early Earth’s environment because it contained no oxygen and was reducing.

2. An oxidizing environment (like Earth’s O2-rich environment today) is corrosive, tending to break molecular bonds. A reducing environment tends to add electrons to molecules, building more complex forms from simple ones. 3. In 1953, American chemist Stanley Miller tested this hypothesis using an artificial mixture of inorganic

molecules (H2O, H2, CH4, and NH3) in a laboratory environment that simulated conditions on the early Earth. 4. Within days, the mixture produced amino acids, some of the 20 amino acids that are found in organisms today. (3.12) 5. More recent experiments, using modifications of Miller’s setup to more closely mimic the early Earth’s environment, have produced all 20 naturally occurring amino acids, sugars, lipids, and nitrogenous bases of nucleotides.

D. The first polymers may have formed on hot rocks or clay (16.4) 1. Polymerization occurs by dehydration synthesis (3.3) 2. Although biological polymerization occurs enzymatically in organisms today, there actions can also occur when dilute solutions of monomers are dripped on hot mineral surfaces (heat forces the dehydration synthesis) or clays (electric charges concentrate monomers, and metallic atoms act as catalysts. 3. American biochemist Sidney Fox has made polypeptides (“ proteinoids ”) from mixtures of amino acids dripped on hot mineral surfaces.

E. The first genes may have been RNA (16.5) 1. The flow of genetic information from DNA to RNA to protein is intricate and probably did not evolve as such. 2. The essential difference between cells and nonliving matter is replication. 3. A number of lines of reasoning and some experiments support the hypothesis that the first genes may have been made of RNA. Short RNA molecules have been created in test tubes without cells or enzymes from precursor nucleotides. Some of these sequences will self-replicate if placed with additional monomer nucleotides. Recent evidence suggests that RNA can act as an enzyme, even one that catalyzes RNA polymerization.

F. Molecular cooperatives enclosed by membranes probably preceded the first real cells (16.6) AP Biology CMR @CHS ‘95 B.Rife page 3 / 9

1. Life requires the close and intricate cooperation of many different polymers. 2. Experimental evidence shows that proteinoids and lipids self-assemble into microspheres, fluid-filled droplets with semipermeable, membrane-like coatings. Though not alive, these microspheres grow by the attraction of additional proteinoids and divide when they reach a certain maximum size. 3. Early molecular cooperation may have involved a primitive form of translation of polypeptides directly from genes in RNA. If these cooperating molecules were incorporated into a microsphere, the basic structures for self-replicating cells would be present. 4. At this point, a primitive form of natural selection would favor those molecular co-ops that were most efficient at growing and replicating.

III. Characteristics of prokaryotes A. Prokaryotes have inhabited the Earth for billions of years (16.7). 1. Fossil evidence shows that prokaryotes (kingdom Monera) were the first living things on Earth 3.5 bya, and they evolved alone for the following 2 billion years. 2. Bacteria are ubiquitous, numerous, and small, surviving in environments that are too hot, cold, acidic, salty, or alkaline for any eukaryote. 3. Despite being small, bacteria influence all other life - as the cause of disease and other problems, as benign inhabitants of all environments, and, more commonly, in beneficial relationships with all other living things. 4. Probably the most essential activities carried out by bacteria are the numerous ways they function in the decomposition of the dead remains (cellular and molecular) of other organisms.

B. Prokaryotes are fundamentally different from eukaryotes (16.8) Two very different kinds of prokaryotes, classified in the domains Bacteria and Archaea are found on Earth today. The most fundamental differences between the organisms of these two domains are in their nucleic acids. 1. Cells are small, typically 1-10 µm wide. Cells lack nuclei. DNA is in the form of a single ring (perhaps with subsidiary plasmids) with little of the complexity and association with proteins found in eukaryotes. (A very large bacterium has recently been discovered as a symbiont in the gut of surgeonfish. Its cells are the largest cells known for nay prokaryote: 500µm long and about 100µm wide, visible to the naked eye.) 2. Sexual reproduction does not occur as a single process. Cellular reproduction is by binary fission, not by mitosis and meiosis. Genetic recombination can occur by several separate processes. 3. Growth rates of colonies of bacteria are exponential; cell numbers double every 10-20 minutes to several hours. The rapid expansion of colony size is checked by the limitation of resources or the buildup of toxic wastes. 4. Cell walls are usually present outside the plasma membrane. the walls are composed of peptidoglycan, a unique, cross-linked polymer found in no other organisms. Some antibiotics interfere with the metabolism of peptidoglycan and are useful in the control of bacteria. C. Bacteria come in a variety of shapes (16.9). AP Biology CMR @CHS ‘95 B.Rife page 4 / 9

1. Cocci are spherical and often occur in defined groups of two or more. 2. Bacilli are rod-shaped and usually occur unaggregated. 3. Vibrios resemble commas, and spirilla and spirochetes are spiral-shaped.

D. Bacteria obtain nourishment in a variety of ways (16.10) 1. Review: Cellular respiration, fermentation (ch 6), and photosynthesis (ch 7) 2. Modes of nutrition refer to how organisms obtain energy and carbon.

3. Autotrophs are “self-feeders” that make carbon compounds from the carbon in CO2 and the energy in sunlight (photosynthesis) or inorganic compounds.

4. Examples of photosynthetic prokaryotes include cyanobacteria that use H2O as a source of electrons and

release O2 as a waste product, and several other groups that use other electron sources, such as H2S. 5. Heterotrophs are “other-feeders” that make carbon compounds from the carbon in existing organic compounds and obtain energy from those same compounds (chemotrophs) or from sunlight. 6. E. coli is an important chemoheterotroph that lives in the human intestine, that can live on simple sugars alone. (An important aspect of the prokaryotes is that, taken as a whole, they exhibit more kinds of metabolic activities (nutritional and otherwise) than are found in organisms in all other kingdoms combined.)

E. The first life forms were probably chemoheterotrophs (16.11) 1. Absorbing nutrients form the environment is chemically simpler than synthesizing them anew. 2. A possible scenario for the evolution of an early form of chemoheterotrophic nutritional metabolism: a) Free ATP is used as a source of energy for early cells b) ATP is used up faster than it can be regenerated by abiotic processes c) the evolution of proteins (enzymes) that catalyzed the synthesis of ATP occurs, using energy stripped from other organic compounds d) the step-by-step evolution of glycolysis occurs 3. This hypothetical scenario is supported by the fact that glycolysis is the only metabolic pathway common to all life, and that it is anaerobic. Various types of fermentation are minor extensions of the glycolytic pathway that became common among bacteria on the early Earth.

F. Archaebacteria are fundamentally different from all other bacteria (16.12) 1. Their ribosomes are different from those of of the bacteria and of eukaryotes. Their plasma membranes contain unique lipids. Their cell walls lack peptidoglycans and therefore are not sensitive to the antibiotic penicillin. 2. Archaebacteria may have evolved very early, as their name suggests, and some scientists think they are so different from other bacteria that they should be classified in a separate kingdom. (Some evidence supports a view that archaebacteria are more closely related to eukaryotes than to other prokaryotes.) AP Biology CMR @CHS ‘95 B.Rife page 5 / 9

3. The methanogens are a group of anaerobic, methane-producing bacteria that thrive in some vertebrate intestines and in the mud of swamps. 4. The halophiles thrive in salt flats and salty lakes. 5. The thermoacidophiles thrive in hot springs at temperatures close to boiling and at low pH. Today, all living prokaryotes except the archaebacteria are classified as eubacteria, a huge group found literally everywhere and upon which all other forms of life depend.

IV Diverse structure features allow bacteria to thrive in various environments (16.13) A. Flagella 1. Review: Eukaryotic flagellum structure and function (4.18) 2. Flagella can be either scattered over a cell or in bunches at one or both ends. 3. Size, structure, and function differ from those aspects of eukaryotic flagella. 4. They are composed of protein in two parts: external, nonmembrane-bounded filaments and rotating rings embedded in the plasma membrane and cell wall. 5. Motion is produced as they spin on their axes like propellers. B. Pili 1. Review: The role of sex pili in conjugation (12.1) 2. Pili are protein filaments thinner than bacterial flagella 3. Pili help bacteria stick to each other or to surfaces in their environments. C. Endospores 1. Spores are single-celled dispersive structures, similar in function to seeds. Thick- walled spores are formed inside the parent cell walls around a replicated copy of DNA. 2. Endospores are extremely resistant to decomposition and disintegration. 3. Clostridium botulinum is a bacterium that grows in anaerobic, low-acid environments, such as poorly canned vegetables. The toxin released by colonies of the bacterium causes botulism when consumed by humans. D. Hyphae 1. Hyphae are tubular filaments from which actinomycetes are constructed. They may be branched and/or divided into many compartments by crosswalls. 2. Actinomycetes are important chemoheterotrophic soil bacteria. Some are commercial sources of antibiotics (streptomycin from Strepomyces bacteria).

V. Additional roles played by prokaryotes. A. Cyanobacteria sometimes “bloom” in aquatic environments (16.14) 1. Blooms are population explosions of microorganisms (usually photosynthetic) in freshwater lakes and marine bays. 2. A bloom of a red species of cyanobacterium gives the Red Sea its name. 3. Large blooms of cyanobacteria indicate that a lake is polluted. Blooms of cyanobacteria can release large amounts of toxins that kill fish.

Blooms of all sorts of microorganisms can use up O2 during nighttime respiration and suffocate other O2 requiring organisms. AP Biology CMR @CHS ‘95 B.Rife page 6 / 9

B. Some bacteria cause disease (16.15) 1. Bacteria cause about half of all known human diseases and are responsible for diseases in all other eukaryotes. 2. Diseases can be caused by bacterial growth on, and destruction of, tissues, but they are more likely to be caused by the release of exotoxins out of growing bacteria or the presence of endotoxins on the surfaces of these bacteria. 3. Staphylococcus aureus is a normal skin bacterium, but when it grows inside a person, the exotoxins it produces can cause serious disease. 4. Species of Salmonella produce endotoxins that cause food poisoning and typhoid fever. (The recent cases of fatal poisonings by a toxic strain of E. coli are due to endotoxins.) 5. The cause of Lyme disease, Borrelia burgdorferi , is carried by a tick and elicits a distinctive set of symptoms (“Bull’s eye rash”) and potential disorders. 6. Sanitation , the use of antibiotics , and education are three of our defenses against bacterial diseases.

C. Koch’s postulates are used to identify disease-causing bacteria (16.16) 1. discovering the bacterial (or protistan, fungal, or animal) cause of disease is the first step in preventing or curing the disease. 2. In 1876, German physician Robert Koch presented diagnostic criteria proving Bacillus anthracis to be the cause of anthrax. a) The same pathogen must be found in each host. b) The pathogen must be isolated into pure culture. c) The original disease must be produced in new hosts inoculated with he culture. d) The same pathogen must be reisolated from the new host. 3. For some pathogens, Koch’s postulates cannot be used because the organism cannot be cultured outside the host. The cause of syphilis, the spirochete Treponema pallidum , is such an organism, but the first postulate is true, and other evidence leaves no doubt that this bacterium is the cause of the disease.

D. Chemical cycles in our environment depend on bacteria (16.17) 1. Because of the variety of metabolic capabilities, bacteria play many beneficial roles in cycling elements amount living and nonliving components of environments. 2. Chemical cycles are discussed more fully in chapter 36.

3. Only bacteria are capable of nitrogen fixation, the conversion of N2 gas to nitrogen in amino acids. Important nitrogen fixers include many cyanobacteria and many chemoheterotrophs in the soil. 4. The breakdown of organic wastes by decomposers is one of the most common beneficial roles of bacteria. 5. Bacterial decomposers are part of the aerobic and anaerobic communities of organisms functioning in sewage-treatment plants.

E. Bacteria may help us solve some environmental problems (16.18) AP Biology CMR @CHS ‘95 B.Rife page 7 / 9

1. Natural bacteria are encouraged, or recombinant strains are used, to decompose away the remains of oil spills on beaches. 2. Species of Thiobacillus, autotrophs that obtain energy from oxidizing ions in mineral, can be used to help remove toxic metals from old mine and industrial waste sites.

F. Summary: Bacteria are at the foundation of life on Earth (16.19) 1. All life depends on bacteria, in both an evolutionary and an ecological sense. 2. Bacteria were not only the first producers of O2 but the first organisms tolerant of increased levels of O2 in the atmosphere. 3. Bacteria are extremely important in nutrient cycles of all kinds..

VI. The eukaryotic cell probably originated as a community of bacteria. (16.20) A. The fossil record indicates the first eukaryotes involved between 1.5 and 1 bya. B. Two hypotheses have been proposed to explain how this happened. 1. The infolding of prokaryotic plasma membranes and the specialization of internal membranes into membrane-bounded organelles. 2. Endosymbiotic cooperation among communities of prokaryotes.

C. Considerable evidence supports the endosymbiotic hypothesis. 1. Mitochondria are similar in size and shape to bacteria and include circular DNA and bacteria-type ribosomes. 2. These organelles replicate in eukaryotic cytoplasm in a manner resembling binary fission. 3. The inner, but not the outer, membranes of these organelles contain enzymes and electron transport molecules characteristic of prokaryotes, not eukaryotes. Endosymbiosis is common today between protists and/or prokaryotes.

D. The two hypotheses are not mutually exclusive. Some organelles, such as the nucleus and endomembrane system, may have evolved by plasma membrane invagination. E. Unicellular eukaryotes and their direct multicellular descendants are called protists (16.21) 1. Protists are diverse, united in one kingdom by their relative simplicity and their eukaryotic cells. 2. As a group, protists are nutritionally diverse, being heterotrophic or autotrophic, but not as diverse as the whole kingdom Monera. 3. Protists are found in all habitats but are most common in aquatic ones. 4. As eukaryotes, their cells are more complex, with many kinds of organelles. 5. Life’s most complex cells belong to the ciliates in this kingdom. 6. Evolutionary, protists were pivotal because it was ancestral protists that evolved into ancestral plants, fungi, and animals.

VII. Heterotrophic protists (protozoans and relatives). AP Biology CMR @CHS ‘95 B.Rife page 8 / 9

A. Protozoans are protists that ingest their food (16.22) 1. Most species are free-living inhabitants of watery environments. A few are causes of dangerous diseases of humans and other animals. Most protozoans have cells that lack cell walls, although some have relatively rigid protein skeletons below their plasma membranes. 2. Amoebas move and feed by means of pseudopodia. 3. Flagellates move by one or more flagella. Species of Trypanosoma are spread by tsetse flies and cause African sleeping sickness when they grow among blood cells. Trypanosomes escape a host’s immune response by changing the molecular appearance of the proteins in the membranes. 4. Apicomplexans are all parasites, some causing serious human disease. Plasmodium species are spread by mosquitoes and cause malaria when they reproduce inside red blood cells. 5. Ciliates are common, free-living forms that use cilia to move and feed. Daily activity is controlled by polyploid macronuclei, and sexual recombination involves diploid nuclei. Cilia are defined as numerous, short flagella-like structures arranged in more complex patterns than flagella.

B. Cellular slime molds have multicellular stages (16.23) 1. The unicellular stage exists as individual, amoeboid cells that feed on bacteria in rotting vegetation, increasing their populations by mitotic cell division. 2. When their food supply runs out, the individual cells mass into a slug-like, multicellular colony. 3. The slugs wander about, moving to an advantageous location to reproduce. Some cells form a stalk below, and others form reproductive spores above. 4. Because they are eukaryotes with a simple developmental sequence, cellular slime molds have played a role in research on cellular differentiation.

C. Plasmodial slime molds have brightly colored stages with many nuclei (16.24) 1. These protists exist in several different forms, including single cells, multinucleate (syncytia) feeding webs, resistant bodies, and multicellular reproductive structures. 2. They are common inhabitants of moist, rotting leaves and dead logs. 3. Life starts as individual amoeboid or flagellated cells (that can change back and forth,depending on the availability of water). As these cells ingest bacteria, they grow into the syncytium. 4. When food runs out, the syncytium mounds up into reproductive structures. Because the nuclei in the feeding stage all divide by mitosis at exactly the same time, some plasmodial slime molds were used in early research on the chemistry of mitosis.

VIII. Autotrophic protists. A. Photosynthetic protists are called algae (16.25) 1. All algae have chloroplasts with chlorophyll a. A variety of accessory photosynthetic pigments causes many algae to be other colors than the typical grass-green color of chlorophyll a. 2. Most algae have cell walls composed of cellulose or silica. AP Biology CMR @CHS ‘95 B.Rife page 9 / 9

3. The morphology of species varies considerably, form single cells to colonial filaments to plant-like bodies (seaweeds). 4. Dinoflagellates are uniquely shaped and move by two flagella in perpendicular grooves. Some dinoflagellates are responsible for toxin-releasing blooms in marine water that known as red tides. 5. Diatoms are unicellular, with uniquely shaped and sculptured silica walls. They are common components of watery environments. 6. The green algae are common inhabitants of fresh water and include a large variety of forms. Green algae share some features with higher plants and are considered to be the plant kingdom’s ancestors.

B. Seaweeds are multicellular marine algae (16.26) 1. Seaweeds are the most complex of the photosynthetic protists. Some have complex bodies with leaflike, stemlike, and rootlike structures, all analogous rather than homologous to similar structures in higher plants. 2. Brown algae include the most complex seaweeds. Some can grow to lengths of 100 m, forming kelp “forests” that are rich with other life. 3. Red algae are most common in tropical marine waters. 4. Some algae are seaweeds, such a Ulva. The reproductive pattern of this algae involves alternation of generations, alternating between haploid gametophytes that give rise to spores by meiosis. 5. This pattern is found among many, but not all, algae and all plants and is important in understanding plant evolution (18.4).

IX. The origin of the three multicellular kingdoms of life. A. Multicellular life may have evolved from colonial protists (16.27). 1. Most multicellular organisms, including seaweeds, slime molds, fungi, plants, and animals, are characterized by the differentiation of cells that perform different activities within one organism. 2. Multicellularity undoubtedly evolved several times within the kingdom Protista. Some of these organisms evolved further into ancestors of the plant, fungus, and animal kingdoms. 3. A hypothetical scenario for the evolution of a multicellular plant or animal from an early protist: a) formation of ancestral colonies, with all cells the same b) specialization and cooperation among different cells within the colony c) delimitation of specialized sexual cells from the somatic cells.

B. Multicellular life has diversified over hundreds of millions of years (16.28) 1. The oldest fossils of multicellular organisms (red algae and invertebrate animals) date from 700 mya. 2. A mass extinction occurred between the Precambrian and Paleozoic eras. 3. Up until 500 mya, life was aquatic and represented by diverse animals and multicellular algae, along with ancestral protists and prokaryotes.