Chapter 19 Bacteria, Archaea, Viruses PDF

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Chapter 19 (Bacteria, Archaea, and Viruses) Three Domains of the living world are: o Bacteria o Archaea Prokaryotes o Eukarya

Regardless of domains, all organisms have: o Cell membranes o Ribosomes o Common metabolic processes such as glycolysis o Semiconservative DNA replication o DNA that encodes for proteins (transcription and translation process) Any shared features implied that: o All life is related, but major differences have also evolved

The major difference between Prokaryotic and Eukaryotic cells: o Prokaryotic cells are lack of membrane bound organelles § Unicellular, small, 1-10 microns § Circular DNA, not contained within a nucleus § Use binary fission as cell division, not mitosis. o Eukaryotic cells have membrane bound organelles, including a nucleus

What does nucleotide sequences of ribosomal RNA genes provide? o R-RNA provide first comprehensive evidence of evolutionary relationships among prokaryotes § rRNA was present in the common ancestor of all life à evolutionary ancient § all free living organisms have rRNA § rRNA plays a critical role in translation in all organisms, so lateral transfer of rRNA genes among distantly related species is unlikely. § rRNA has evolved slowly enough that gene sequences from distantly related species can be aligned and analyzed.

Why studying lateral gene transfer can help understand phylogenetic relationships of Prokaryotes? o Lateral gene transfer phenomenon suggests that some genes have been moving “sideways” from one prokaryote species to another.

o Whole genome sequencing has revealed a stable core of crucial genes. Gene trees based on these reveal the organismal phylogeny more accurately What kind of genes are most likely to be involved in lateral gene transfer? o Genes that confers higher fitness on a recipient species are most likely to be transferred repeatedly among species. o Example: genes that produce antibiotic resistance are often transferred among bacterial species on plasmids, especially under the strong selection pressure such as that imposed by modern antibiotic mediations à because improper or overly frequent use of antibiotics can select for resistant strains of bacteria that are much harder to treat. Prokaryotes: Bacteria and Archaea (Prokaryotes are far more abundant than Eukaryotes.) Classification of Bacteria: o Can be divided into two groups based upon nutrition strategyà autotrophs, and heterotrophs. Classification of Archaea: o Similar to bacteria: but, lack peptidoglycan in cell walls, peptidoglycan is unique to bacteria. o Many Archaea are “extremophiles” § Hyperthermophiles § Methanogens § Halophiles

Bacteria have different types of cell walls: o Gram- positive: Ø The thickness of cell wall helps retain the gram stain (blue/purple)

o Gram-negative: Ø Thin wall of peptidoglycan surrounded by lipid membrane- does not retain the gram stain à picks up the counterstain and turns to color red/pink Ø Penicillin cannot reach peptidoglycan layer Three common shapes of bacteria are:! o Sphere à coccus o Rod à bacillus o Spiralà spirillum ** Other shapes include filaments, and branched filaments.

Why do Prokaryotes are considered as the most successful organisms on Earth? o Consider the number of prokaryotes versus eukaryotes.

The eight major bacterial groups are: o Low- GC gram positives o High- GC gram positives o Hyperthermophilic bacteria o Hadobacteria o Cyanobacteria o Spirochetes o Chlamydias o Proteobacteria 1. o o o

Low- GC Gram Positives (Firmicutes): Low ratio of (G-C) to (A-T) nucleotide base pairs in DNA Some are gram negative, some have no cell wall One group of Low-GC Gram positives can produce heat resistant resting structures known as à endospores. Endospores can survive for 1,000 years. Ø Endospores production is not a reproductive process, it replaces the parent cell when key nutrients such as nitrogen and carbon are needed. Ø Endospores can survive in unfavorable conditions that would kill the parent cell. § When in favorable condition, the endospore becomes metabolically active and divides, forming new cells that are like the parent cells. o Includes Clostridium and Bacillus. Bacilus Anthracis: o produces an exotoxin that causes anthrax. o Endospores reactivate and release toxins into the bloodstream when they sense macrophages in mammalian blood. o Have been used as a à bioterrorism agent because large quantities of its endospores can be transported in a small space and spread among human populations, where they may be inhaled or ingested. Staphylococcus: o are abundant on skin and cause boils and other skin problems. S.Aureus is the best known human pathogen in this genus, present in 20-40% of adultsà cause respiratory, intestinal, and wound infections. Mycoplasmas: o no cell wall, extremely small, small genome o less DNA than other prokaryotes o M.Pneumoniae typically mild in adult humans, hence walking pneumonia o M. Ovipenumoniae often deadly in bighorn sheep populations 2. High- GC Gram Positives (Actinobacteria): o Higher ratio of (G-C) to (A-T) nucleotide base pairs in DNA o Branched filaments à the structure breaks up into cocci or bacilli, then reproduce by binary fission. o High GC gram positives also reproduce by forming reproductive spores at filament tips o Most antibiotics come from this group o Include Mycobacterium Tuberculosis à causes tuberculosis, oldest known human pathogen.

Extremophilies are bacteria that live in extreme conditions: o Includes Hyperthermophilic Bacteria and Hadobacteria 3. Hyperthermophilic Bacteria: o Live at extreme high temperatures such as hot springs, volcanic vents, underground oil reservoirs, similar to ancestral conditions on Earth. 4. Hadobacteria: o Deinococcus members survive cold as well as hot temperatures and are resistant to radiation. They can consume nuclear waste. o Thermus Aquaticus members was isolated from a hot spring; source of the thermally stable DNA polymerase used in the development of the polymerase chain reaction. 5. Photosynthetic Bacteria à Cyanobacteria: o Photosynthetic; have blue and green pigments. o Involves in nitrogen fixation o Same photosynthesis processes as in eukaryotes à carried out on an internal membrane system called photosynthetic lamellae. o Chloroplasts of eukaryotes are derived from an endosymbiotic cyanobacterium 6. Spirochetes are gram-negative bacteria o Gram-negative; motile o Have unique axial filaments (modified flagella) that rotate à provide shape and motility o Many spirochetes are human parasites, some are pathogens that cause Symphilis and Lyme disease. 7. Chalamydias live in cells of other organisms o Gram-negative; extremely small o Obligate parasites resulted from an inability to produce ATP o Limited capacity of ATP can be changed using an enzyme translocase, which allows them to take up ATP from the cytoplasm of their host in exchange for ADP from their own cells. o Complex life cycle with two different forms of cells à elementary bodies and reticulate bodies o Various strains of chlamydias cause eye infections, sexually transmitted diseases, and pnesumonia. o 8. Proteobacteria are a large and diverse group of bacteria o Include many species of Gram negative autotrophs that use light-driven reactions to metabolize sulfur, as well as dramatically diverse bacteria that bear no phenotypic resemblance to the photoautotroph species. o Mitochondria of eukaryotes were derived from a proteobacterium by endosymbiosis Ø Genetic and morphological evidences o Escherichia Coli is one of the most studied organisms o Human pathogens: Ø Yersinia Pestis (which causes bubonic plague) Ø Vibrio Cholerae (cholera) Ø Salmonella Tryphimurium (gastrointestinal disease)

How do we aware of the separation of Archaea from Bacteria and Eukarya? o The separation was originally based on phylogenetic relationships determined from sequences of rRNA genes. A common feature between Archaea and Bacteria: o Like bacteria, archaea typically possess a single circular chromosome containing several thousand genes and no introns. Differences between Bacteria and Archaea: o Bacteria and archaea are never pathogenic à no known examples of archaea that form parasitic relationships with a host. o Archaea do not form spores, however bacteria do. o Archaea do not have peptidoglycan in their cell walls à instead, the presence of lipids of distinctive composition in their cell membranes (ether linkages). Characteristics of Archaea: o Live in extreme habitats such as those with high salinity (salt content), low oxygen concentrations, high temperatures, or high or low pH. o Divided into two principal groups: Crenarchaeota and Euryarchaeota. When this substance is formed within cells, the cells become more difficult to kill: o This substance is known as biofilms à cells bind to a solid surface and secrete a sticky polysaccharides matrix that traps other cells Why are cells in biofilms are hard to kill? o The film may be impermeable to antibiotics Where can biofilms be formed? o Can form on any surface, including contact lenses, artificial joint replacements, metal piples. Dental plaque and stromatolites are biofilms. Biofilm formation can be triggered by what process? o Prokaryotes use chemical signals to communicate with one another and trigger density-linked activities such as biofilm formation. Type of communication that prokaryotes use to trigger biofilm formation: o Quorum Sensing: when the population density increases, concentration of the signal increases.

Health of humans and eukaryotes are depended on the health of this mechanism: o This mechanism is known as à Microbiomes o Microbiomes are communities of bacteria and archaea form complex associations with other organisms, these can be mutualistic, communalistic, or parasitic Ø Commensalistic: one organism benefits and the other is not affected Ø Mutualistic / Symbiotic: occur when both the bacteria and the host benefit from the interaction § Mitochondria and gut flora are examples of symbiotic relationships Why is gut flora useful to human body? o Breaking down undigested carbohydrates, synthesizing vitamins B and K, and many other vital biological functions. Why is gut flora useful to immune system? o Useful in training the immune system, preventing the growth of harmful bacteria, and regulating the production of important fat-storing hormones. Imbalances or damage to gut flora can lead to? o Is implicated in a wide range of human pathologies à Inflammatory bowel disease, obesity, colitis, cancer, and even mental health

How do microbiomes affect our health? o Affect gene expression, and play a critical role in development and maintenance of a healthy immune system Microbiomes are affected by what factors? o Affected by our diets, medicines, and exposure to toxins

A small number of bacteria are considered as à Pathogens o Pathogenic bacteria are harmful because they either reproduce uncontrollably inside human cells or produce dangerous toxins.

What are the rules for establishing that a particular microorganism causes a particular disease? o Koch’s Postulates. o These rules were used to show that ulcers are caused by the bacterium Helicobacter pylori. What are the four key ideas to satisfy Koch’s Postulates? The microorganism must be present in every case of the disease ⇒ Results: Biopsies from the stomachs of many patients revealed that the bacterium was always present if the stomach was inflamed or ulcerated. The microorganism can be taken from the host and grown in pure culture ⇒ Results: The bacterium was isolated from biopsy material and eventually grown in culture media in the laboratory. The isolated and cultured bacteria must be able to induce the disease when injected into a new, healthy host ⇒ Marshall was examined and found to be free of bacteria and inflammation in his stomach. After drinking a pure culture of the bacterium, he developed stomach inflammation à Gastritis. The bacteria must be recoverable from newly infected individuals ⇒ Biopsy of Marshall’s stomach 2 weeks after he ingested the bacteria revealed the presence of bacterium, now christened Hylicobacter pylori, in the inflamed tissue. For the host, the consequences of a bacterium infection depend on what factors? o Invasivness of the pathogen: à ability to multiply in the host’s body. o Toxigenicity à ability to produce toxins (chemical substances that are harmful to the host’s tissues). What are the two general types of bacterial toxins? How is it released? o Endotoxins: released when certain Gram-negative bacteria grow or burst (lyse). This toxin consists of a polysaccharide and a lipid component that form part of the outer bacterial membrane. ⇒ Rarely fatal, they cause fever, vomiting, and diarrhea. ⇒ Examples: Salmonella, and Escherichia o Exotoxins: released by living, multiplying bacteria. This toxin are soluble proteins. ⇒ Highly toxic, often fatal. Small doses used for cosmetic or muscle spasms purposes. ⇒ Examples: § Tetanus à Clostridium Tetani § Choleraà Vibrio Cholerae § Bubonic Plague à Yersinia Pestis § Anthrax à Bacillus Anthracis § Botulism à Clostridium Botulinum • Most poisonous Great diversity of metabolic pathways is led by?

o Long evolutionary history of bacteria and achaeaà more time to explore a wide variety of habitats Anaerobic metabolism in Prokaryotes à Anaerobes Anaerobes do not use oxygen as an electron acceptor in respiration. o Obligate Anaerobes: oxygen is poisonous to these organisms. o Facultative Anaerobes: ability to use both aerobic and anaerobic metabolic pathways o Aerotolerant Anaerobes: cannot conduct aerobic cellular respiration, but they are not damaged by oxygen when it is present. Some prokaryotes require oxygen for cellular respiration: o Obligate Aerobes: unable to survive for extended periods in the absence of oxygen. Require oxygen as an electron acceptor in cellular respiration.

Four broad nutritional categories of organisms: o Photoautotrophs: perform photosynthesis à use carbon dioxide as carbon source ⇒ Cyanobacteria use chlorophyll a and produce oxygen ⇒ Others use bacteriochlorophyll and produce sulfur, not oxygen. § Hydrogen Sulfide (H2S) is their electron donor for photophosphorylation. § Bacteria using the bacteriochlorophyll pigment can grow in water under fairly dense layers of algae. o Photoheterotrophs: use light as their energy source, however they obtain carbon from organic compounds made by other organisms à Carbohydrates, fatty acids, and alcohols. ⇒ Sunlight provides the energy necessary for metabolism through photophosphorylation. o Chemoautotrophs: obtain energy from oxidizing inorganic substances and using it to fix carbon ⇒ Some bacteria oxidize à ammonia, nitrite, hydrogen gas, hydrogen sulfide, sulfur, and other materials. ⇒ Many archaea are chemoautotrophs o Chemoheterotrophs: obtain both energy and carbon atoms from one or more complex organic compounds that have been synthesized by other organisms. ⇒ Most known bacteria and archaea are chemoheterotrophsà as are all animals, fungi, and many protists.

Why do many biologists do not consider viruses as living organisms? o Viruses are not cellular, and must depend on cellular organisms for basic life functions such as replication, and metabolism. Viruses are what type of parasites of living cells? What are their functions/features? o Obligate parasites. o Use the same essential forms of genetic information storage and transmission Viruses infect what type of organisms? o ALL forms of life à bacteria, archaea, and eukaryotes § replicate, mutate, evolve, and interact with other organisms. o Viruses evolve independently of other organisms, so there’s no way to treat them as a a part of living organisms. Population of viruses? How does it affect the eco system? o Extremely abundant à 1000 times more viruses than the number of living organisms on the planet. o ½ of the bacteria in the oceans are killed by viruses each day. ⇒ Huge bacteria blooms such as the bioluminescent Vibrio, are soon followed by blooms of viruses. What are the factors that make viruses phylogeny? o Small genomes restrict phylogenetic analyses o Rapid mutation and evolution rates cloud evolutionary relationships over long periods o No known fossils because of their size o Highly diverseà viruses may evolved repeatedly within each of the major groups of life o Grouped based on genome structure (DNA, RNA) not how we grouped other organisms. Features of Viruses: o The genetic material of viruses can be DNA or RNA o Single stranded (ssRNA or ssDNA) or double stranded (dsRNA or dsDNA) o Most animal viruses such as HIV, Influenza, Ebola, Rhinovirus, and plant viruses are ssRNA, while most bacteria- infecting viruses (bacteriophages) are dsDNA.

Features of RNA retroviruses: o Single stranded RNA (ssRNA), probably evolved as escaped cellular components. o Reproduce/Regenerate through reverse transcription ⇒ DNA is produced and integrated into the host genome, where it is replicated along with the host’s DNA ⇒ The integrated viral DNA is known as à Provirus o Only infect vertebrates; includes HIV, and some are associated with various cancers. What happens when retroviruses become incorporated into host genomes? o Many become nonfunctional copies that are no longer expressed as functional viruses. What do nonfunctional retroviruses sequences provide? o A record of ancient viral infections o Humans have about 100,000 fragments of endogenous retroviruses in our genome à greater fraction of the genome than the protein-coding genes. What are viruses that infect and destroy bacteria? o Bacteriophages Features of Bacteriophages: o Bacteriophages are harmless to humans o One drop of seawater à contains one million bacteria, and ten million bacteriophages. Most bacteriophages will use what structure of DNA as genetic material o Double stranded DNA (dsDNA)

Viruses Applications: o Viruses can be used to introducing genetic material inside a cell à biotechnology o Research to use bacteriophages to treat antibiotic resistant bacterial infections (phage therapy) and even cancer (virotherapy) Prokaryotes vs. Microorganisms: o Microorganisms and microbes are catch all terms that include any microscopic life form ⇒ These terms include Bacteria, Archaea, but also Protists, and depending on the definition, viruses. o Protists are Eukaryotes....