Prokaryotes: Bacteria and Archaea Dr. Corl BIOL 106 January 26, 2011 Introduction Let?s begin our study of the tree of life by examining in detail: Lack a membrane bound nucleus*. Include Domain Bacteria and Domain Archaea. Introduction Three domains of life: Bacteria and Archaea (all prokaryotes) Eukarya* (all eukaryotes) Note that: Until relatively recently, prokaryotes were all grouped into a single Kingdom: Monera*. Sequencing and comparison of genetic material shows, however, that Archaea* are more closely related to eukaryotes than they are to bacteria! Introduction Basic characteristics of prokaryotes: Lack* a nuclear envelope. Possess a single*, double-stranded DNA chromosome that is circular. Microscopic*! Almost all are unicellular organisms. Introduction Prokaryotes can be found in a hugely wide range of environmental conditions. Extremophiles: Prokaryotes that live in high-salt, high temperature, low temperature, or high-pressure habitats. Extreme thermophiles* thrive in high temperature environments (e.g. 90?C in the hot spring above!). Extreme halophiles* live in highly saline environments. Overview Prokaryotic morphology: What do prokaryotes look like? Importance of prokaryotes: Why do we care about prokaryotes? Metabolic diversity: How do prokaryotes obtain nutrition? Major lineages of prokaryotes Prokaryotic Cells Plasma membrane: Encased by a Cell wall: Gives organism shape and support. Surrounds the Cytoplasm: Interior contents of the cell. Flagellum: Used for movement. Prokaryotic DNA Most genes are contained on a single, circular, DNA-containing Chromosome. NO nulcear* membrane. Prokaryotes may also have a few other genes in small, circular plasmids. Prokaryotic Ribosomes Ribosomes: Made up of RNA and protein* molecules. Important for manufacturing proteins*. Some antibiotics* (e.g. tetracycline) act by selectively interfering with bacterial ribosome function. Differences Between Prokaryotes and Eukaryotes Eukaryotic cells: e.g. Protist, plant, animal, and fungal cells. House DNA in a membrane-bound nucleus*. Are usually much larger* than prokaryotic cells. Contain extensive internal* membranes. Have a diverse and dynamic cytoskeleton*. Usually replicate via mitosis. Binary Fission Prokaryotes replicate via binary fission: 1.) Chromosome* is replicated. 2.) Each chromosome copy moves towards a different pole (end) of the parent cell. 3.) Ring of contractile proteins (FtsZ proteins) assembles near cell?s ?equator.? 4.) FtsZ ring constricts*, causing parent cell to pinch into two daughter cells. What do Prokaryotes Look Like? Great diversity* in prokaryotic morphology! Basic Shapes Coccus (plural: cocci): spherical*. Bacillus* (pl.: bacilli): rod-shaped. Spirillum (pl.: spirilla): Corkscrew*-shaped. Organization of Cells Many prokaryotes occur singly*. Others are arranged in clusters*: Diplo- : two (e.g. diplococcus) cells together. Strepto-: chain*-like arrangement of cells. Staphylo-: grape*-like cluster of cells. Bacteria and Archaea: Similarities Lack a membrane-bound nucleus. Have a singular, circular DNA* chromosome. Almost all are unicellular*. Many move using flagella*. Have a cell wall. However, cell wall composition is different! Bacteria Archaea Bacteria and Archaea: Differences Cell wall composition: Bacteria (not Archaea) cell walls include peptidoglycan*. Archaea share the following characteristics with Eukarya, but NOT with bacteria: DNA associated with histone* proteins. Start codon specifies for methionine (not formylmethionine). RNA polymerase* relatively complex. Bacteria Archaea The Gram Stain Using the Gram Stain* procedure, bacteria can be divided into two broad subcategories: Gram-positive bacterial cells stain purple*. Gram-negative bacterial cells stain pink*. The Gram Stain: Procedure Crystal violet (purple dye) is selectively retained* by Gram positive* cells. Why? Gram + cells and Gram - cells differ in the amount of peptidoglycan* in their cell walls. The Gram Stain Gram positive bacteria have a thick* peptidoglycan layer in their cell walls: Crystal violet dye is retained within the cytoplasm*, staining the bacteria purple*. The Gram Stain Gram negative bacteria have a thin* peptidoglycan layer in their cell walls: Crystal violet dye is NOT retained within the cytoplasm, and can be easily washed* away with alcohol. Gram negative cells can be subsequently dyed pink using a different stain, the counterstain safranin*. The Gram Stain Medical relevance: Useful tool in helping to identify* bacteria. Helps determine what antibiotic* can be used to treat a particular infection: e.g. Penicilin* blocks peptidoglycan cross-linkage --> effective in killing Gram + cells. Summary Thus Far Prokaryotic morphology: Components of a typical prokaryotic cell. Basic shapes and organization. Comparison between Domains Bacteria and Archaea. Gram Stain procedure for bacteria. Importance of Prokaryotes Why do we care about prokaryotes? They live on and in us! ~ 10 billion live on our skin. ~ 100 trillion live in our intestines*, some of which help us to digest the food we eat. Used to convert* milk to cheese and yogurt. Important component of ecosystems. Some bacteria are pathogenic* (cause disease). E. Coli* is a model organism in laboratories. Escherichia coli E. coli is a model organism that is studied in many laboratories: Easy* to raise in liquid broth or on nutrient agar. Important* every 30 minutes by binary fission. Useful for studying the mechanisms underlying many life processes, including: DNA replication and repair Transcription* and transcription factors Translation and ribosomal functioning Pathogenic Bacteria Bacteria cause ~50% of human diseases. E.g. Lyme disease and syphilis, caused by spirochete* bacteria (above). Pathogenic bacteria may: Secrete toxic proteins while alive (exotoxins*). Release toxic molecules upon dying (endotoxins*). No achaea* are known to cause disease in humans?however: Presence of certain archaea is correlated with a human gum disease: periodontitis. Koch and the Germ Theory of Disease Until the mid-1800s, many doctors believed in the miasma theory of disease: Postulated that infection diseases were caused by poisonous vapors or ?bad air.? Robert Koch proposed an alternative theory, the vapors* of disease, in the late 1800s: Postulated that infectious diseases are caused by bacteria* and viruses*. Koch?s Postulates Using the following 4 criteria, Dr. Koch demonstrated that anthrax* in cattle is caused by a Gram positive bacteria, Bacillus anthracis. 1.) The microbe must be found specifically in diseased* animals and not in healthy animals. 2.) The microbe must be isolated* and grown in pure culture away from the host organism. 3.) The cultured microbe, upon injection* into a healthy host, should cause disease symptoms to appear. 4.) The microbe, upon isolation from the new host, should be identical to the original organism in 1.) Pathogenic Bacteria Pathogenic bacteria include: Gram + bacteria that cause: Anthrax,?staph*? infections, strep throat, leprosy. Gram - bacteria that cause: Syphilis*, chlamydia, gonorrhea, ulcers*, plague. Prokaryotes: Ecosystem Biology Many prokaryotes are important decomposers*: Break down dead organisms and return nutrients to the abiotic environment. Some prokaryotes are photosynthetic* and are primary producers: Synthesize ATP and sugars using inorganic molecules and energy from sunlight*. Prokaryotes as Decomposers Prokaryotes are important components of webs*! Cleaning up Pollution Organic* compounds released or leaked into the environment by humans: e.g. Petroleum* from oil spills. Can be highly toxic* to human and other lifeforms. Can be very difficult* to clean up: Do not dissolve easily in water. Highly resistant to decomposition --> just ?sit there.? Cleaning up Pollution Researchers are exploring bioremdiation*: Using bacteria and archaea to degrade* pollutants. Encourage* prokaryotic growth at polluted site by: Fertilizing contaminated sites to encourage growth of pollutant eating bacteria. Adding specific prokaryotes to the contamination site. e.g. Used oil-eating bacteria to clean up the small oil spill on the left side of the picture above. Prokaryotes and the Nitrogen Cycle Prokaryotes play essential roles in the Nitrogen* cycle: Atmospheric* nitrogen (N2) is fixed by certain bacteria into a form that is usable to plants* (NO3-: nitrate). Plants convert nitrate to organic forms (e.g. amino acids) that are usable by consumers. Prokaryotes and the Nitrogen Cycle Prokaryotes play essential roles in the nitrogen cycle: Denitrifying* bacteria, using nitrogen-containing compounds as a final electron acceptor in cellular respiration, return nitrogen to the atmosphere* as N2. Prokaryotes as Primary Producers Cyanobacteria*: aka ?blue-green algae.? Perform oxygenic photosynthesis*: Like plants, cyanobacteria produce oxygen* (O2) as a byproduct of photosynthesis. Prokaryotes as Primary Producers Data indicates that cyanobacteria* were responsible for putting oxygen* into the earth?s atmosphere about 2 billion years ago! Atmospheric oxygen then made aerobic cellular respiration* a possibility. Metabolic Diversity Prokaryotes are extremely metabolically diverse: Can use a wide variety* of resources to meet their 2 primary nutritional needs: Synthesizing molecules of ATP*. Synthesizing macromolecules*: e.g. carbohydrates, lipids, proteins, and nucleic acids Synthesizing ATP: Phototrophs Phototrophs*: E.g. Cyanobacteria (blue green algae) Use light* energy to help synthesize ATP*. Synthesizing ATP: Chemotrophs Chemoorganotrophs: Oxidize organic* molecules (e.g. glucose*) to make ATP through cellular respiration. Chemolithotrophs: Oxidize inorganic* molecules (e.g. ammonia, methane, or H2S) to make ATP through cellular respiration. This mode of nutrition is unique* to prokaryotes! Synthesizing Macromolecules Autotrophs*: Can synthesize macromolecules using very simple* building blocks (e.g. CO2, CH4). e.g. Cyanobacteria can synthesize sugars from CO2 via the Calvin cycle of photosynthesis. Heterotrophs*: Must obtain organic building-block compounds from other organisms*. Summary Prokaryotes have six general methods of obtaining energy* (ATP) and carbon*. Note: Eukaryotes* fall into only 2 categories: Photoautotrophs (e.g. plants). Chemoorganoheterotrophs (e.g. animals). Variations on Photosynthesis Some prokaryotes perform oxygenic* photosynthesis: e.g. Cyanobacteria (blue-green algae). Use water as an electron donor. Produce oxygen* as a byproduct of photosynthesis. Others perform anoxygenic* photosynthesis: Use a molecule other* than water as an electron donor (e.g. H2S or Fe2+). Produces S or Fe3+ as a byproduct instead of O2. Variations on Cellular Respiration Recall that cellular respiration generates ATP* through a series of redox reactions involving: An electron donor (e.g. glucose*). An electron transport chain. A final electron accpetor*(e.g. O2). Variations on Cellular Respiration Many prokaryotes, however, use an electron donor* other than sugar and use an electron acceptor* other than oxygen! Overview Prokaryotic morphology: What do prokaryotes look like? Importance of prokaryotes: Why do we care about prokaryotes? Metabolic diversity: How do prokaryotes obtain nutrition? Major lineages of prokaryotes Bacteria: Key Lineages Gram negative* bacteria: Cyanobacteria Proteobacteria Spirochaetes and Chlamydiales Gram positive* bacteria (Firmicutes and Actinobacteria) Cyanobacteria Also known as blue-green* algae. All perform oxygenic* photosynthesis. Can occur singly, in long chains, or in clusters of cells (colonies*). Responsible for putting oxygen into the atmosphere of ancient earth! Proteobacteria Diverse in morphology and metabolism. Some can aggregate* to form elaborate fruiting bodies tipped with resistant spores. Some members live in close association with plant roots and perform nitrogen fixation*. Some cause disease*: E.g. Gonorrhea, ulcers, food poisoning (Salmonella). Other Gram Negative Bacteria Spirochetes*: Corkscrew-shaped cells (Spirillium* shape). Can cause syphilis and Lyme disease. Chlamidiales*: Live inside* animal cells as endosymbionts. Cause the sexually transmitted disease, chlamydia. Gram Positive Bacteria Many are free-living soil species: decomposers*. Some used to ferment* milk into yogurt and cheese. Some can form a durable resting stage, an endospore*, to survive harsh environmental conditions. Some cause disease*: Anthrax, strep throat, walking pneumonia, leprosy. Archaea Two major lineages: Crenarchaeota and Euryarchaeota. No known pathogenic* species?however: Certain Euryarchaeotans linked with human gum disease rRNA sequencing has shown that archaea are more related to eukaryotes* than they are to bacteria! Archaea Some archaeans are extremophiles*: Able to live in very harsh* environmental conditions. e.g. Extreme thermophiles*, extreme halophiles, and acid-loving species. Crenarchaeota in a hot spring Euryarchaeota in a salt pond Summary Prokaryotic morphology: What do prokaryotes look like? Importance of prokaryotes: Why do we care about prokaryotes? Metabolic diversity: How do prokaryotes obtain nutrition? Major lineages of prokaryotes Review Questions Compare and contrast: Prokaryotes vs. eukaryotes Bacteria vs. Archaea Describe the Gram stain - you?ll be using it in lab this week! How do various prokaryotes meet their primary nutritional needs: Obtain ATP Obtain carbon for building macromolecules
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