Chapter 26
Explain the ecological diversity impacts of the environment
THE OXYGEN REVOLUTION -the oxygen we breath comes from cynobacteria which first became numerous in teh ocean 2.7-2.5 billion years ago, and the first organisms to perform oxygenic photosynthesis -the fossil record and geologic record indicate that oxygen concentrations in teh oceans and atmosphere began to increase 2.3-2.1 billion years ago -once oxygen was common, cells could began to use it as the final electron acceptor in cellular respiration, which made aerobic respiration possible. -Because oxygen is extremely electronegative, it is an effiecent electron accpetor, which means much more energy can be released as electrons move through the electron transport chain -once oxygen was avaiable, cells could produce much more ATP for each electron donated by NADH and FADH2, energy production rose as a result -cyanbacteria were respondsible for a fundamental change in Earth's atmosphere- oxygen allowed the production of the ozone layer, which protects earth's surface from ultraviolet radiation, making evolution of life on land possible NITROGEN FIXATION AND THE NITROGEN CYCLE -Orgaisms must have nitrogen to synthesize proteins and nucleic acids -though the nitrogen in the atmoshere cannot be used because of the strong triple bond linking the nitrogen atoms -Certain bacteria and archaea are only organisms capable of converting molecular nitrogen to ammonia, this process called nitrogen fixation -this process is highly endergonic reduction-oxidation reactions. The key enzyme that catalyzes the reaction-nitrogenase- is found only in a few phyla bacteria and archaea. Many of these organisms are free-living, but some form important relationships with plants: --some species of cynobacteria live in an association with a water fern that grows in rice paddies amd help fertilize the rice plants --in terrestrial environments, nitrogen-fixing bacteria live in close association with certain plants-often taking up residence in speical root structures called nodules -- the only organisms with the nitrogenase gene are those that live in anaerobic habitats or are able to protect the enzyme from O2 -Bacteria and archaea use a wide array of nitrogen-containing compunds as electron donors and electron acceptors during cellular respiration -to understand why this is important, consider htat nitrate produced by some bacteria as a by-product of respiartion does not build up in the environment. -Instead, other species of bacteria and archaea use it as an electron donor, and it oxidized to molecular nitrate. -Nitrate, in turn, is reduced to molecular nitrogen by yet another suite of prokaryotic species. In this way, bacteria and archaea are responsible for driving the movement of nitrogen atoms through ecosystems around the globe in a process called nitrogen cycle NITRATE POLLUTION -Farmers use fertilizers that are high in nitrogen because crops do not live in association to nitrogen-fixing bacteria. -In parts of the world, massive additions of nitrogen in the form of ammonia are causing serious pollution problems -Nitrates As A Pollutant: 1. Ammonia is introduced as a ferilizer 2. Corn uses some of Nh3 to build protein. Soil-dweeling bacteria and archaea uses NH3 as an electron donor 3. Nitrate, a by-product of respiration, enters groundwater and washes into rivers 4. NO3 from runoof stimulates blooms of marine algae and cynobaceria 5. When cells that bloomed eventually die, decomposers such as bacteria and archaea grow rapidly, using up oxygen 6. Anoxic dead zone
Explain the metabolic diversity amoung prokaryotes
-producing ATP through Cellular Respiration-variation in electron donors and acceptors --glucose is the original eletron donor and oxygen is final electron acceptor- this scenario is aerobic --molecules with high potential energy serve as electron donors and molecules with low-potential energy act as electron acceptors- these reveal variety -producing ATP via Phosphorylation:Variation in Electron Sources and Pigments --1. Light activates a pigment called bacteriorhodospin or archaerhodopsin, which uses the absorbed energy to transport protons across the plasma membrane and out of the cell . The resulting flwo of protons back into the cell drives the synthesis of ATP into chemiosmosis --2. A recently discovered bacterium that lives near hydrothermal vents on teh ocean floor performs phosphorylation not by aborbing sunlight, but by absorbing faint light from geothermalo radiation --3. Pigments that absorb light raise electrons to high-energy states. As these electrons are stepped down to lower energy states by electron transport chains, the energy released is used to generate ATP. Researchers have isolated nine different chlorophyll pigments from different lineages of bacterial phototrophs. Each lineage has one or more of these distinctive chlorophylls. This prcoess requires electrons. In photosyntheisis in cynobacteria and other plants, the electrons come from water. When these organisms split water molecules apart to obtain electrons they release oxygen as a by-product. Species that use water as a source use oxygenic photosynthesis. Phototrphic bacteria use a molecule other than water, so they perform Anoxygenic photosynthesis -Obtaining Building-Block Compunds: Variation in Pathways for Fixing Carbon --Enzymes of the Calvin Cycle transform carbon dioxide into organic molecules that can be used in synthesizing cell material . However, not all autotrophic bacteria and archaea use the Calvin cycle to make building-block molecules , and not all start with CO2 as a source of carbon atoms. For example, consider these biochemical pathways: -some bacteria are called methanotrophs because they use methane as a carbon source- and as a elctron donor in cellular respiration. -some archaea are considered methanogens. These organisms produce methane as a by-product of cellular respiration . The foramtion of methane in the guts of humans and other mammals is largely due to the activity of methanogens.
Explain how prokaryotes obtain building-block compunds with carbon-carbon bonds-the two different ways
1. AUTOTROPHS- synthesize their own compunds from simple starting material such as CO2 and mehtane 2. HETEROTROPHS- absorb ready-to-use organic compounds-called building block compounds- produced by other organisms in their environment
Explain how Bacteria and Archaea acquire energy- the three different ways
Bacteria and Archaea acquire energy to produce ATP in three ways: 1. PHOTOTROPHS-use light-energy to excite electrons. ATP is produced by phosphorylation 2.CHEMOORGANOTROPHS- oxidize organic molecules with high potential energy , such as sugars. ATP is produced by cellular respiration-with sugars serving as electron donors or via fermentation pathways 3.CHEMOLITHOTROPHS-oxidixe inorganic molecules with high potential energy such as ammonia, or hydrogen sulfide. ATP is produced by cellular respiration, and inorgainc compounds serve as electron donors
Describe the major taxa of Bacteria
ACTINOBACTERIA- are filamentous, forming branching chains; htey are adundant in soil and are important decomposers of dead plants and animal material; some live in association with plant roots and fix nitrogen; others can break down toxins like herbicides, nicotine, and caffiene; antimicrobal compunds have been isolated from species which are prescribed to treat diseases in humans and livestock CHLAMYDIAE- may be the least diverse of bacterial lineages. Only 13 species are known- all spherical and very small. They live as parasitic endosymionts CYANOBACTERIA-- photosynteic bacteria are found as indepedent cells, in chains that form filaments, or loose agregations of individual cells called colonies. They are the most sbundant organims on Earth. They produce much of the oxygen, nitrogen, and organic compunds htat feed organisms living in freshwater and marine enviroments FIRMICUTES-are extremely common in animal intestines, where they live in symbiotic mutualism, aiding the digestive process. Several species play useful roles in agriculture and food processing; others cause a varitey of human disease PROTEOBACTERIA-some species formed stalked cells, while others form aggregates of cells organized as spore-forming fruiting bodies. While several species cause disease, other play key roles in cycling of nitrogen atoms through terrestrial and aquatic ecosystems SPIROCHAETES-unique corkscrew shape and flagella. Their flagella are contained within a structure called the outer sheath, which surronds the shell.Parasictic, disease-causing species are propelled by this motion into the tissues of their host. Other spirochete species are extremely common in freshwater and marine habitats. And one species is found only in the hindgut of termites, where it fixes nitrogen
Antibiotics- past, present , and future
Antibotics are molecules that kill bacteria or stop them from growing. They are produced naturally by a wide-array of soil-dwelling bacteria and fungi. Antibiotics are hypothesized to help cells reduce for competition for nutrients and other resources.Extensive use of antibiotics in the late twentith century in clinics and animal feed led to the evolution of drug-resistant strains of pathogneic bacteria. New research indicates that bacteria have another advantage: they usually grow as biofilms-dense bacterial colonies enmeshed in a polyssacharide-rich matrix helps shield the bacteria from antibiotics.
Prokaryotic cell-wall composition- what's the difference between bacterial and archaea composition?
Archaea have unique phospholipids in their plasma memebranes, the hydrocarbon tails are made from isoprene Bacteria have a unique compund called peptidoglycan in their cell walls
Exlpain why bacteria and archaea are considered the most important , diverse, and abundant organisms on Earth
Bacteria and archaea were on Earth long before multicellular life appeared. They are ubiquitous and have highly diverse metabolic activities. This diversity allows different species within clades to inhabit every imaginable surface where there is sufficient moisture. For example, some estimates suggest that in the typical human body, bacterial cells outnumber human body cells by about ten to one. Indeed, bacteria and archaea comprise the majority of living things in all ecosystems. Certain bacterial and archaeal species can thrive in environments that are inhospitable for most other life. Bacteria and archaea, along with microbial eukaryotes, are also critical for recycling the nutrients essential for creating new biomolecules. They also drive the evolution of new ecosystems (natural or man-made).
Explain how prokaryotes live in extreme environemnts
Bacteria or Archaea that live in high salt, high temperature, or high pressure habitats are extremeophies Some organisms have developed strategies that allow them to survive harsh conditions. Almost all prokaryotes have a cell wall, a protective structure that allows them to survive in both hypertonic and hypotonic aqueous conditions. Some soil bacteria are able to form endospores that resist heat and drought, thereby allowing the organism to survive until favorable conditions recur. These adaptations, along with others, allow bacteria to remain the most abundant life form in all terrestrial and aquatic ecosystems. Prokaryotes thrive in a vast array of environments: Some grow in conditions that would seem very normal to us, whereas others are able to thrive and grow under conditions that would kill a plant or an animal. Bacteria and archaea that are adapted to grow under extreme conditions are called extremophiles, meaning "lovers of extremes." Extremophiles have been found in all kinds of environments: the depths of the oceans, hot springs, the Arctic and the Antarctic, in very dry places, deep inside Earth, in harsh chemical environments, and in high radiation environments ((Figure)), just to mention a few. Because they have specialized adaptations that allow them to live in extreme conditions, many extremophiles cannot survive in moderate environments. There are many different groups of extremophiles: They are identified based on the conditions in which they grow best, and several habitats are extreme in multiple ways. For example, a soda lake is both salty and alkaline, so organisms that live in a soda lake must be both alkaliphiles and halophiles ((Figure)). Other extremophiles, like radioresistant organisms, do not prefer an extreme environment (in this case, one with high levels of radiation), but have adapted to survive in it ((Figure)). Organisms like these give us a better understanding of prokaryotic diversity and open up the possibility of finding new prokaryotic species that may lead to the discovery of new therapeutic drugs or have industrial applications.
Describe the major taxa of Archaea
Crenarchaeota -The Crenarchaeota are Archaea, which exist in a broad range of habitats. They are tolerant to extreme heat or high temperatures. They have special proteins that help them to function at temperatures as high as 230 degrees Celsius. They can be found in deep-sea vents and hot springs, regions with superheated water. These include thermophiles, hyperthermophiles, and thermoacidophiles. Euryarchaeota -These can survive under extremely alkaline conditions and have the ability to produce methane, unlike any other living being on earth. These include methanogens and halophiles. Korarchaeota -They possess the genes common with Crenarchaeota and Euryarchaeota. All three are believed to have descended from a common ancestor. These are supposed to be the oldest surviving organism on earth. These include hyperthermophiles. Thaumarchaeota -These include archaea that oxidize ammonia. Nanoarchaeota -This is an obligate symbiont of archaea belonging to the genus Ignicoccus.
Describe how some pathogenic bacteria produce resistant endospores
Endospores are tough-thick walled, dormant structures formed during times of environmental stress, often in response to a lack of nutrients. They contain a copy of teh cells DNA, RNA,ribosmes, and essential enzymes that become surronded by a tough, resistant wall.. Once walled off from the surronding cell, metabolic activity within t eh endospore stops and the rest of the original cells breaks down. Endospores are resistant to high temps, UV radiation, and even antibiotics. When conditions become favorable, endospores resume normal growth, becoming actively dividing cells Some bacterial endospores are involved in transmitting disease to humans. EX'S are tetanus, gangrene, botulism, and anthrax Cattle, herbivores, and humans can ingest these endospores can develop anthrax or any other disease that they consume
Explain how genetic variation is introduced in prokaryotes Desribe gene transfer and the 3 ways it occurs:
Genetic variation through gene transfer: lateral gene transfer is central to the evolution of bacteria and archaea. Through this process , prokaryotes can acquire diverse traits that would not be otherwise be avaiable when cells divide through binary fission. gene transfer occur in three ways: 1 Transformation-when bacteria or archaea naturally take up DNA from the environment that has been released by cell lysis or secreted 2. Transduction-when viruses pick up DNA from one prokaryotic cell and transfer it to another cell 3. Conjuation- when genetic inforamtion is transferred by direct cell-to-cell contact
What does the Gram charge tell you about the bacteria sample?
Gram-positve cells may respond to treatment by penicillin-like antibiotics that disrupt peptidoglycan synthesis since these cells contain peptidoglycan Gram-negative cells are more likely to be affected by erthromycin or other types of anti-biotics that poision bacterial ribosomes
Explain the relationship between microbiomes and human health
Human microbiome encompasses all the microbes that inhabit the body or parts of the body, such as mouth, gut, and other tissues. Some biologists are even exploring the ancient micobiome preserved on fossilized human teeth. Humans harbor a diverse ecosystem of symbiotic prokaryotes. the human gut microbiome alone is composed of 100 trillion bacteria and archaea that play a key role in human healt. We depend on microbes to stay healthy. Cahnges in teh gut microbiome have been linked to both inflammatory bowel disease and obesity.
Describe Koch's postulates
Koch was the first person to establish a link between a particular species of bacterium and a specific disease. To establish cauasative link betweena specific microbe and a specific disease, Koch proposed that four criteria had to be met: 1. The microbe must be present in individual's suffering from the disease and absent from healthy individuals. Koch later abandoned this absolute requirement when he discovered that, in some,cases infectious microbes could be present in a individual who was nearly or completely free of signs of disease 2.the organism must be isolated and grown in a pure culture away from the host organism. koch used a nutrient medium and using gelatin as a substrate 3. If organisms from the pure culture are injected into a healthy experimental animal, the disease symptoms should appear. 4. The organism should be isolated from teh diseased experimetnal animal, again gorwn in pure cu;ture, and demonstrated by its size, shape, and color to be the same as teh orginal organism. These criteria are still used in modified form to confirm a causitive link between new diseases and a suspected infectious agent. They have changed because microbiologsts now recognize that many bacteria cannot be gown in culture, so they use other means of detection for those organisms, such as DNA sequence-based identification
Describe the Germ Theory
Koch's experiemtnal results were the first test of the germ theory of disease. It states that infectious diseases are caused by specific microbes in the body-such as bacteria, archea, and viruses. infectious diseases are spread in three main ways: 1. Some are passed from person to person 2. some are transmitted by bitesfrom insects or animals 3. Some are acquired by ingesting contaminatd food or water, or being exposed to microbes in teh surrinding environment. The germ theory laid the foundation for modern medicine, it's gratest impact was on sanitation-efforts to prevent transmission of pathogenic bacteria.
Explain the role of bacteria in bioremediation
Microbes play an important role in waste-water treatment, and researchers are using them to clean up sites polluted with organic solvents- an effort called bioremediation. Naturally existing populations of bacteria and archaea can grow in spills and degrade the toxins . This growth can be enhanced using two complementary bioremediation strategies: 1. fertilizing contaimanted sites to encourage the growth of exisiting prokaryotes that degrade toxic compunds ( biostimulation)- After several oil spills, researchers added nitrogen to affected sites as a fertilizer. Dramatic increases occured in the growth of bacteria and archea that use hydrocarbons in cellular respiration, probably because the cells used the added nitrogen to synthesize enzymes and other key compounds. 2 Seeding-or adding- specific species of prokaryotes to contaminated sites. Seeding shows promise of alleviating pollution in some situations. Researchers have recently bacteria that can ender harmless certain chlorinated compunds EX'S-London's Olympic Park, Deepwater Horizon oil spill
Gram-positive and gram-negative- what does it have to do with cell wall and plasma memebrane coposition?
Most cells that are gram-positive have a plasma membrane surronded by cell wall with an extentsive peptidoglycan-which is a coplex substance composed of carbohydrate strands that are cross-linked by short chain of amino acids Most cells that are gram-negative have plasma membranes surronded by a cell wall that has two components - a thin gelatinous layer containing peptidoglycan and an outer phospholipid bilayer
Explain how phylogenies are used to study relationships amoung prokaryotes
Phylogenetic trees for the Bacteria and Archaea have been based on studies of teh RNA molecules found in a small subunit of ribosomes. Carl Woese's phylogenetic tree is considered a classic result- and the major division were acknowledged to be Bacteria, Archaea, and Eukarya, when before organisms were just divided into prokaryotes and eukaryotes. Domain bacteria and Domain Archea are two separate monophyletic groups and Domain Eurkarya shares a common ancestor with Acrhaea
Describe the characterisitcs of prokaryotes
Prokaryotes lack an organized nucleus and other membrane-bound organelles. Prokaryotic DNA is found in a central part of the cell called the nucleoid. The cell wall of a prokaryote acts as an extra layer of protection, helps maintain cell shape, and prevents dehydration. Prokaryotic cell size ranges from 0.1 to 5.0 μm in diameter. The small size of prokaryotes allows quick entry and diffusion of ions and molecules to other parts of the cell while also allowing fast removal of waste products out of the cell.
Describe the structural features of prokaryotes
SIZE- can range from 0.15 um to 200*10^16 um^3 SHAPE AND ARRANGEMENT- can be filaments, spheres, and rods, and even spirals. They are arranged in chains or clusters MOTILITY- many bacterial cells are motile; moved by rotating flagella. Bacterial flagella spin like a propller rather than eukaryotic flagella which move back and forth, bacterial cells can glide as well but we don't know what causes this
Explain how metabolic diversity of bacteria and archaea can explain how these organisms thrive in a wide array of habitats
The array of electron donors, accpetors, and fermentation substrates they exploit allow heterotropihic prokaryotes to live anywhere The evolution of three types of phosphorylation-based on bacteriorhodpsin or archaerhodopsin, geothermal energy, or pigments that donate high energy electrons to ETC's- extends the types of habitats that can support phototrophic prokaryotes
Describe how metagenomics is used to study prokaryotes
To augment research-based on enrichment cultures, biologists are employing a technique called metagenomics or environmental sequencing. metagenomics is being used to catalog all the genes present in a mixed community of prokaryotes. it's based on extracting and sequencing much of DNA from an environmental sample that contains numerous unknown species. Genes present in teh community are identified by comparing the DNA sequeces with those of known genes. In this way, previously undiscovered species, genes, ans biochemical pathways can be characterized. 1. collect samples from an environment containing a mixed community of unknown organisms and extract DNA. 2. generate small DNA fragments and sequence as many as possible 3. Compare these sequences with those of known genes. this information can be used to identitfy species and investigate biological processes
What makes some bacterial cells pathogenic?
Virulence, or the ability to cause disease, is a heritable trait that varies amoung individuals in a population. The genome of the pathogenic strain is slightly larger because it has acquired virulence genes, including one coding for a proetin toxin. After entering a host cell, this toxin binds to ribosomes and inhibits protein synthesis , killing the host cells Because of key differences between the ribosomes of bacteria and eukaryotic cells, only the host's- not the bacterium's- protien synthesis is blocked by the toxin. Cells lining the blood vessels near the host's intestinal epithilum are most affected by teh toxin, and the resulting damage, and resulting damage leads to bloody diarehha and possible death. if sanitation is poor, the pathogenic bacteria are likely to infect many new hosts- this is true for E coli.