Final Exam Study Guide - Introduction to Microbiology | MICR 2123, Study notes of Microbiology

Download Final Exam Study Guide - Introduction to Microbiology | MICR 2123 and more Study notes Microbiology in PDF only on Docsity! MICRO 2123 Review Sheet for Exam #1. Chapters 2: Microscopy • Know Hooke and Leeuwenhoek’s importance to microscopy o Hooke: § Constructed the first compound microscope § Published the first illustration observed through a microscope § Coined the term “cell” § First to see microbes in a microscope (eukaryotes) o Leeuwenhoek: § Designed powerful microscopes allowing him to search for microbes in unexpected habitats § First to see bacteria (prokaryotes) • Magnification vs Resolution o Magnification- means an increase in the apparent size of an image to resolve smaller separations between objects § How much bigger it is than it is in real life o Resolution- the smallest distance by which two objects can be separated and still be distinguished § Always limited by the human eye • Bright field vs dark field microscopy – Know that you have to have stain with bright field and you can see small images on dark field o Bright-field microscopy generates a dark image of an object over a light background § To increase resolution: use shorter wavelength light, lessen contrast, use immersion oil, use wider lens closer to specimen, higher numerical aperture o Dark field microscopy- optics enables microbes to be visualized as halos of bright light against darkness § Light shines at oblique angle § Only light scattered by sample reaches objective § Makes visible objects below resolution limit (flagella, very thin bacteria) • Why would I use a fluorescence microscope o The light that comes in are absorbed by the molecule then the molecule goes to a higher energy state o Incident light is absorbed by the specimen and reemitted at a lower energy, thus lower wavelength o Can see specific subcellular components • TEM vs SEM o Transmission electron microscopy (TEM)- electrons pass through the specimen and reveals internal structures § The TEM closely parallels the design of the bright-field microscope § Magnetic fields are used to focus electrons § Florescent screens are used for detections § Provides internal details in 2-D o Scanning electron microscopy (SEM)- electrons scan the specimen surface and reveals external features in 3-D § Arranged somewhat differently from the TEM § Generally smaller Chapter 3: The Bacterial Cell • Define cell membrane, cell wall, nucleoid, selective transport, passive transport, active transport, chemotaxis. o Cell membrane- encloses the cytoplasm; the structure that defines the existence of a cell; semipermeable barrier o Cell wall- covers the cell membrane o Nucleoid- non-membrane-bound area of the cytoplasm that contains the chromosome in the form of looped coils. § Important function of the cell envelope is to contain and protect the cell’s genome o Selective transport- essential for survival because it prevents a cell from coming to equilibrium; no movement leads to death o Passive transport- molecules move along their concentration gradient; no energy is required o Active transport- molecules move against their concentration gradient; required energy (ATP) o Chemotaxis- the movement of a bacterium in response to chemical gradients; § Attractants cause CCW rotation, flagella bundle together, push cell forward, “swim” § Repellents cause CW rotation, flagellar bundle falls apart, “tumble”= bacterium briefly stops, then changes direction • Know the structure of peptidoglycan – a polymer of the disaccharide NAG-NAM bound to a 4 aa peptide that is cross linked to give the cell wall rigidity. NAM-NAG….tetrapeptide……that is cross linked between strands. o Peptidoglycan § Backbone chain (alternating N-acetyle muramic acid [NAM] and N-acetyl glucosamine [NAG] § Cross link bound to NAM: • Gram negative (4 amino acids, crosslink between DAP and D-Ala) o L-Alanine o D-Glutamate o Diaminopimelic acid [DAP] o D-Alanine • Gram positive (9 amino acids, cross link being a 5-Gly bridge between Lys and D-Ala) o L-Alanine o D-Glutamate o L-Lysine o D-Alanine o Glycine (5 of these as part of crosslink) • NAG-NAG-NAG = chitin (structure in yeast and plants; skeleton in insects) o Peptide extends from nuramic acid o Alpha 1-4 glycogen (store sugar) o Beta linkage between sugars o NAM energy-beta linage • PG in Gm+ vs Gm- • D vs L amino acids…..which one is unique to PG. o L will fit though ribosome-translation o D is unique to bacteria, peproglyca • Where is teichoic acid and what is purpose o Used for strength and rigidity; the gram positive cell wall is made up of 20-30 layers of peptoglycan o Amino acid cross-links in peptidoglycan o Found outside the plasma membrane • Capsule? o Gram positive cell envelope- not all species have them o Made of polysaccharides o The outside is slimy which makes it slick and hard for things to kill it because it cannot be grasped. • Why do I care that mycobacteria have mycolic acid? o Mycolic acid- target mycolic acid to get rid of TB (slow growing and takes a while to heal) o Maycobacterial cell envelopes include unusual membrane lipids (mycolic acids) and unusual sugars (arabinogalactans) • Know what is in the outer membrane of Gm- o Bacteria (thin cell wall); cell wall thickness is based on the amount of peptoglycan present o • Extremophiles o an organism that thrives in physically or geochemically extreme conditions that are detrimental to most life on Earth • Psychrophiles o Grows in temperatures between 0-20°C o “loose” proteins and an “oily” cell membrane from unsaturated fatty acids • Mesophiles o Grows in temperatures between 15-45°C o Most of the bacteria you will encounter fit here • Thermophiles o Grows in temperatures between 40-80°C o Very stable proteins and less fluid cell membrane with saturated fatty acids • What is the main cellular structure that changes between the optimal growth temps of these? o All of these organisms have membranes and proteins best suited for their temperatures • Why can’t psychrophiles survive at thermophile temps? • Does internal pH change for alkaliphiles like the internal temp of a thermophile? Why? How do bacteria manage the extreme pHs? o Alkalphiles- grow above pH 9 o Thermophile- grows between 50-80 degrees C. • Know classifications on Microbial Responses to Oxygen slide – slide 15. o Strict aerobes can only grow in oxygen o Microaerophiles grow only at lower O2 o Strict anaerobes die in the least bit of oxygen o Facultative anaerobes can live with or without oxygen o Aerotolerant anaerobes grow in oxygen while retaining a fermentation-based metabolism • Sterilization vs disinfection vs antisepsis vs sanitation o Sterilization- killing of all living organisms o Disinfection- killing or removal of pathogens from inanimate objects o Antisepsis- killing or removal of pathogens from the surface of living tissues o Sanitation- reducing the microbial population to safe levels • Pasteurization….why do I care? o Kills pathogens o Ex: dairy products • Joseph Lister’s claim to fame. o Developed carbolic acid to treat wounds and clean surgical instruments; prevented deaths from infection • Define antibiotic. Why do I care? And why do I care that I take them all? o Antibiotics- chemical compounds synthesized by one microbe that kill or inhibit the growth of other microbial species • Water activity- a measure of how much water is available for use Chapter 6, 11: Virology • What is a virus? o Oblifatory intacellular parasites- contain DNA (single-stranded or double stranded) or RNA (single stranded [+ or -] or double stranded) o Contain a protein coat (coats outside of virus) o Some are enclosed by an envelope o Some viruses have spikes o Most viruses infrect only specific types of cells in one host • Life cycle of the virus o Host recognition and attachment o Genome entry o Assemble of virions o Exit and transmission • Protein coat? Host Range? Capsid? Envelope? o Protein coat- coats outside of the virus o Host range- o Capsid- composed of repeated protein subunits § Packages the viral genome and delivers it into the host cell o Envelope- formed from the cell membrane § Contains glycoprotein spikes which are encoded by the virus • Lytic vs lysogenic cycles o Lytic- Bacteriophage quickly replicates, killing host cell o Lysogenic- bacteriophage is quiescent § Integrates into cell chromospmes, as a prophage § Can reactivate to become lytic • Transduction? Prophage…use of prophage • Types of viral genomes o DNA or RNA o Single or double stranded (ss or ds) o Linear or circular • DNA virus o Can utiliza the host replication machinery • RNA o Use an RNA-dependent RNA-polymerase to transcribe their mRNA • Retroviruses o Use a reverse transcriptase to copy their genomic sequence into DNA to insertion in the host coromosome • 6 steps of animal virus life cycles. o Attachment § Viruses attach to cell membrane o Penetration § By Endocytosis or fusion o Uncoating § By viral or host enzymes o Biosynthesis § Production of nucleic acid and proteins o maturation § Nucleic acid and capsid proteins o Release § by budding (enveloped viruses) or rupture • RNA viruses use an _RNA_-dependent RNA polymerase to transcribe their mRNA • Retroviruses use a _reverse transcriptase_to copy their genomic sequences into DNA. • HSV primary infection is _epithelial_but latent infection can occur within_neurons of ganglia__. Why is this important to you? • Poliovirus is transmitted by _fecal-oral__route. Most cases result in mild _gastrointestinal__________________. __1___% result in paralysis. First vaccine was the Salk vaccine which uses a _______________viral particle whereas the Sabin vaccine uses a ______________virus. If you were in class, you can tell me the advantages of each. I’m sure Wiki has it otherwise…. • Influenza A has a _segemnted_genome. Why is this important? H stands for _Hemagglutinin____ while N stands for _Neuraminidase____ and why do I care? • What is a reverse transcriptase and why do I care? • Contrast acute, latent and persistent viral infections. An example of each would be suggested. o Acute- fight infection § Ex: influenza, small pox o Persistent § Ex: HIV o Latent § Herpes, shingles • Norovirus and Rotavirus cause ______________and are especially fatal in ____________of the _____________world. • Lipopolysaccharide (LPS) is unique to gram negative • Microbe groups: bacteria, archaeam algaem protists, fungi MICRO 2123 Sp 2012 Review Sheet for Exam #2 Chapter 7: Genomes and Chromosomes • Define Genome, Vertical and Horizontal gene transmission, structural gene vs DNA control sequence, operon o Genome: all of the microbe's hereditary information o Vertical Gene Transmission: parent to child gene transmission o Horizontal Gene Transmission: transfer of small pieces of DNA from one cell to another o Structural Gene: encodes for a functional RNA, which usually encodes a protein o DNA Control Sequence: regulates the expression of a structural gene, does not encode RNA o Operon: a functioning unit of genomic DNA containing a cluster of genes under the control of a single regulatory signal or promoter. • DNA is a polymer of 4 deoxynucleotides which are adenine, thymine, cytosine, and guanine. • DNA Strands come together in an anti-parallel fashion • Define Topoisomerase and why is it important to DNA replication. o Topoisomerase: enzymes that over-wind DNA or under-wind it § Over-wind: allow cells to pack more DNA in a tight space § Under-wind: allow cells to transcribe DNA by unpacking it • DNA Synthesis o Replication begins at a single ori site and ends at a termination site. o Know the 6 enzymes of DNA replication and their function. § Helicase: first DNA replication enzyme, separates the two DNA strands § DNA Primase: second DNA replication enzyme, lays down a short stretch of complementary RNA (primer) • Primer: stretch of complementary RNA during DNA replication § DNA Polymerase III: third DNA replication enzyme, makes DNA at the primer § RNase H: fourth DNA replication enzyme, removes the primer § DNA Polymerase I: fifth DNA replication enzyme, replaces RNA primer with DNA § Missense: class of mutation where it changes the amino acid sequence to another, making the protein not fold correctly § Nonsense: class of mutation where it changes the amino acid sequence to a stop codon § Frame-shift: class of mutation where it changed the open-reading frame of the gene • Define Transposable elements o move from one DNA molecule to another Chapter 10 Molecular Regulation • Define Repressors, Operators, Activators, Inducers, Repressors, co-repressors, Derepression, aporepressor o Repressors: protein that binds to regulatory sequences (operators) in the DNA and prevent transcription of target genes o Operators: o Activators: protein that binds to regulatory sequences in the DNA and stimulate transcription of target genes o Inducers: o Depression occurs when repression goes down, happens when the corepressor (ligand) levels go down, thus the corepressor is released from the aporepressor, thus making it unable to bind to the operator, allowing transcription to occur. • Understand the difference btw Activation, Repression and Induction. o Activation: occurs when an inducer (ligand) binds to an activator protein, which then binds binds to the activator sequence o Repression: o Induction: occurs when an inducer binds a repressor • What is a two component signal transduction system ….sensor kinase vs response regulator o Two-component signal transduction systems (TCST system): systems that sense the external environment o Sensor kinase: part of the TCST system in the cell membrane that binds to environmental signals and phosphorylates itself o Response regulator: part of the TCST system in the cytoplasm that takes phosphate from sensor and binds the chromosome to alter transcription for multiple genes • How does the lac operon work? Ara operon? Trp operon? o Produced when protein (lactose) levels are low o Lac operon: required for the transport and metabolism of lactose in some bacteria o Ara C – repressor – looks like the sticky thing you throw at the wall. Has the ability to bend the DNA o When there is no arabinose, the dna is bent and you get no transcription or translation of the structural genes o Lac protein is lacI; ligand is allolactose; induction is what its called o Ara; AraC; arabinose; activation o Trp; TrpR; tryptophan; repression • How does attenuation work in the trp operon? o if tryptophan is absent, a different structure forms, thus the Trp operon is transcribed o if tryptophan is present, a Rho-independent transcription terminator stem loop forms. o When a Rho-independent transcription terminator stem loop forms, transcription is stopped, the Trp operon is not expressed. • How do sigma factors control transcription and give a couple examples o Sigma factors bind to the core RNA polymerase or RNA pol falls off o Sigma factors recognize the promoter o Heat-shock sigma factors transcribes heat-shock genes o Sporulation sigma factors translate sporulation genes o Sigma factors also bind to the promoter • What is gene arrangement? Example? • Define chemotaxis and how does it work? o Behavior in which motile bacteria swim toward favorable environments (like food sources) o In chemotaxis, bacteria move via a random walk, which is caused by swims and tumbles. • What is quorum sensing and how does it work and what is an autoinducer? Examples are? o Quorum sensing: process where bacterial cells work together at high density o In quorum sensing, the autoinducer is secreted and diffuses away atlow bacterial density, but it accumulates at high bacterial densities and various autoinducers diffuse back into the cells to bind an activator protein, that then changed the transcription of genes o Quorun sensing is used by Vibrio fischeri within squid to make them glow Chapter 6, 11: Virology • What is a virus? o Obligatory intracellular parasite. Contain DNA or RNA • Protein coat? Host Range? Capsid? Envelope? o Protein coat: the substance that protects a virus's genetic material and helps it get inside a cell o Host Range: range of organisms a virus can infect o Capsid: packages viral genome and delivers it to the host cell § Encoded by the virus genome, made by the host o Envelope: made from cell membrane, covers the capsid in some viruses • Lytic vs lysogenic cycles o Lytic: bacteriophage quickly replicates, killing host cell rapidly o Lysogenic: bacteriophage is inactive, integrates into cell chromosome using prophage, can reactivate to become lytic • Transduction? Propage…use of prophage o Transduction: the process in which infection by a virus results in DNA being transferred from one bacterium to another o Prophage: the viral DNA that is embedded in the host cell's DNA • Types of viral genomes o DNA or RNA, double or single strand, linear or circular o DNA Viruses - can utilize host to replicate machinery o RNA Viruses - use RNA dependent RNA-polymerase to transcribe their mRNA o Retroviruses - use reverse transcriptase to copy their genome into DNA for insertion into host chromosone • 6 steps of animal virus life cycles. 1.) Attachment 2.) Penetration 3.) Uncoating 4.) Biosynthesis 5.) Maturation 6.) Release • RNA viruses use an RNA-dependent RNA polymerase to transcribe their mRNA • Retroviruses use a reverse transcriptase to copy their genomic sequences into DNA. • HSV primary infection is epithelial but latent infection can occur within neurons of the ganglia Why is this important to you? o Most common STD in US • Poliovirus is transmitted by fecal-oral route. Most cases result in mild gastrointestinal infection. 1% result in paralysis of which 15% die. First vaccine was the Salk vaccine, which uses a whole kill viral particle whereas the Sabin vaccine uses a live intenuate virus. If you were in class, you can tell me the advantages of each. I’m sure Wiki has it otherwise…. o Any live vaccine can revert and cause illness, whole kill is more effective o Sabin can convert back to wild type • Influenza A has a segmented genome. Why is this important? H stands for Hemagglutinin while N stands for Neurominidase . and why do I care? o Segmented genome causes quick evolution o H1N1 o Tamiflu targets the N • What is a reverse transcriptase and why do I care? o RNA to DNA o First major class of drugs found helpful in slowing HIV are called reverse transcriptase inhibitors o Only that can change RNA to DNA • Contrast acute, latent and persistent viral infections. An example of each would be suggested. o Acute: short term with rapid recovery – influenza o Latent: dormant for years before appearing or reappearing – HPV o Persistent: constantly present in the system - HIV • Norovirus and Rotavirus cause diarrhea and are especially fatal in children of the developing world. 5’ end is phosphate; 3’ hydroxyl group off of DNA MICRO 2123 Sp 2012 Review Sheet for Exam #4 Chapter 17: • What is a clade…………group of species with a common ancestor. • How divergence occur………random mutations and reductive evolution • In constructing a phylogenetic tree, it is essential to align your sequences • Trees could either be rooted or unrooted depending on the use of an outgroup • Know on a tree where is the node and where is the branch • Universal genes using for constructing trees 16S (bacteria) and 18S (eukaryotes) SSU rRNA • What are the 3 domains of life? Bacteria, Archaea, Eukaryotes 3. Gram-positive bacteria- Have thick cell walls that retain the Gram stain – crystal violet. Walls are reinforced by teichoic acids. a) Firmicutes. a. Spore-forming: Bacillus, Clostridium. One aerobic and one anaerobic. Both form spores upon starvation or stress. b. Non spore-formers: for each one on slide 7 of non-spore formers know the name, the O2 tolerance and one example i. Listeria monocytogenes 1. Facultative anaerobic ii. Lactic acid bacteria 1. Aerotolerant obligate fermenters a. Lactobacillus or Lactococcus iii. Staphylococcus 1. Facultative anaerobes a. S. aureus iv. Streptococcus 1. Aerotolerants a. S. pneumonia b) Actinobacteria- can be identified by the acid-fast stain due to the presence of mycolic acid in their cell walls. a. Mycelial: i. Streptomyces- obligate aerobes 1. Form mycelia that fragment into smaller cells called Arthrospores. b. Nonmycelial: i. Mycobacterium- rod shaped cells & have thick wells with mycolic acids 1. TB 4. Gram-negative bacteria- Only the Proteobacteria. 5 classes. Only discussed 4 of them. All share a common structure – their triple-layered Gram-negative cell envelope. Outer membrane; cell wall (periplasm); and cell membrane. Have very diverse metabolism. For slides 10-13, know the modes of metabolism (e.g. heterotroph, phototroph, lithotroph, and so on) and one example for each. • Alphaproteobacteria: • Photoheterophs- (Rhodobacter) o Purple bacteria containing bacteriochlorophyll with accessory carotenoids. • Methylotrophs & methanotrophs- (Methylobacterium) o oxidize single-carbon compounds. • Endosymbionts- (live inside the host) o Mutualists: N2-fixers and plant roots (Rhizobium) o Parasites: Intracellular pathogens (Rickettsiales) § This clade also includes mitochondria For the beta, gamma, and delta similarly know the metabolism modes and one example. • Betaproteobacteria o Photoheterotrophs- (Rhodocyclus) o Lythotrophs § Nitrifiers that oxidize ammonia to nitrite • Nitrosomonas: used in wastewater treatment. Decrease the dissolved N ontent § Sulfur and iron oxidizers • Thiobacillus oxidize sulfide to sulfate o Pathogens § Neisseria gonorrhoeae (humans) • Gammaproteobacteria o Sulfur and iron phototrophs § Chromatium anaerobic phototroph • Use sulfide and produce sulfur, which is deposited as cytoplasmic granules o Sulfur lithotrophs § Beggiatoa oxidizes H2S to sulfur, which collects as periplasmic granules o Facultative anaerobes § Enterobacteriaceae. Aerobic or anaerobic respiration § Can ferment rapidly on carbohydrates § Escherichia coli • Some strains grow normally in the intestine o Aerobic rods § Obligate respirer either aerobic or on nitrate § Pseudomonas species have polar flagella and are vigorous swimmers • Deltaproteobacteria o Myxococcus xanthus § Soil bacteria that can grow as isolated cells or aggregate into fruiting bodies (if starved) § Can disperse spherical myxospores o Bdellovibrio species § Parasitizes proteobacterial cells § Penetrates into periplasm, where it uses host resources to grow o Sulfur and Iron reducers § Lithotrophs § Geobacter reduces iron § Desulfuromonas reduces elemental sulfur § Desulfobacter reduces sulfate 5. Planctomycetes- Peptidoglycan-less cell wall. Some have a double membrane that surrounds the nucleoid, analogous to a nuclear membrane 6. Verrucomicrobia- Have peptidoglycan cell walls. Have a cytoskeleton that appears to contain tubulin. Genes must have arisen through horizontal transfer from a eukaryote. • Archaeal diversity: Surprisingly, the archaeal domain lacks pathogens Distinctive features of archaea “archaeal signatures” include: o Cell membrane lipids- Ether-linked o Cell wall components- Pseudopeptidoglycan. o Certain metabolic pathways- Methanogenesis, Bacteriorhodpsin. 1. Phylum Crenarchaeota- wider range of temperature (Hyperthermophiles, thermophiles, mesophiles, and psychrophiles) 2. Phylum Euryarchaeota- great range of metabolism i. Methanogens- Strictly anaerobic. Major substrates include: 1. Carbon dioxide: CO2 +4H2 -> CH4 + 2H2O A. Assimilation. Process by which organisms acquire an element to build into cells from an inorganic source, e.g. Carbon from CO2. o CO2 fixation, N2 fixation o Organisms are called primary producers and their role is: o Absorbing energy from outside the ecosystem, e.g. phototrophs o Assimilating minerals into biomass, e.g. autotrophs B. Dissimilation. Process of breaking down organic nutrients to inorganic minerals, e.g. CO2 • What determines the kind of assimilation /dissimilation occurring in an ecosystem? A. Availability of electron acceptor o Aerobic respiration is dissimilatory. Anaerobic respiration allow slower rates. Lithotrophy coupled to autotrophy is assimilatory (Fix Co2 and provide energy and organic carbon) B. Environmental conditions: Temperature, pH, and salt o Higher temp fastest growth rate • All organisms participate in the food web. Beside the primary producers, there are: Grazers (primary consumers), Predators (secondary consumers), and at each trophic level, bodies of dead organisms are consumed by decomposers. • Symbiosis is an intimate association between organisms in different species. Mutualism is a symbiotic relationship where the 2 partners benefit and may fail to grow independently. Know the lichens example. o Lichens is a mutualism between an algae (or cyanobacteria or both) and a fungus § Algae or cyanobacteria provide photosynthetic nutrients § Fungus provide protection § Cyanobacteria also fixes nitrogen § For dispersal, the lichen form asexual clumps of algae wrapped in fungal mycelia • Syntrophy: A special case of symbiosis where there is a metabolic association requiring both partners to complete the metabolism with a negative ΔG. A type of mutualism. Know the termite gut example. o Termites have endosymbiotic bacteria that digest wood polysaccharides such as cellulose § Wood polysaccharides are converted by gut bacteria and protists to fermentations products including CO2 and H2 § Methanogens use CO2 and H2 to produce CH4 § In the absence of methanogens, CO2 and H2 accumulate inhibiting the growth of fermentative bacteria § In the absence of fermentating bacteria, methanogens can not grow § This kind of mutualism is called syntrophy • Ecosystems we studied: For the marine and soil know who the primary producers are and who the consumers are. In marine, decomposers are viruses. In soil, decomposers are bacteria and fungi. A. Marine- Ocean zones a. The ocean floor: selects for barophilic psychrophiles except around black smokers where barophilic thermophiles live. In black smokers upwelling of reduced H2S, H2, as well as CO2. Four players interact: i. Sulfate-reducing bacteria (SRBs) reduces sulfate from seawater with the H2 upwelling with the fluid producing sulfide ii. Sulfide is then oxidized by sulfide-oxidizing lithotrophs (SOBs). SOBs are associated with animal hosts (worms, anemones, and clams) in a symbiotic relationship where bacteria fix CO2and provide organic carbon while reducing the level of poisonous sulfide at the same time. iii. Methanogens use CO2 and H2 to produce CH4 iv. Methane produced support methanotrophs B. Soil- Layers and who survive in each a. Mycorrhizal fungi- WHY? Benefits to the plant and to the fungi- Extend access of plants to minerals & also help distribute organic substances between different plants b. Ectomycorrhizae- i. Colozie the rhizoplane (surface of plant rootlets) ii. Fungai ycelia never penetrate the root. They form a thick mantle on the root surface and extend mycelia away from the root to absorb nutrients iii. Ex: Ascomycetes as truffles c. Endomycorrhizae- i. Fungi penetrate plant cells forming an arbuscle within a root cell ii. Exist entirely underground iii. Ex: Zygomycetes genus Glomus C. N2-fixing Rhizobium in plant roots. A form of bacteria-plant mutualism. Know what each of these mean: a. Bacteroid- no cell wall b. Symbiosome- Sac of plant derived membrane for protection c. Leghemoglobin- sequesters excess O2 gas and supplies just the amount needed for aerobic respiration without poisoning nitrogenase D. Microbial community in rumen- Major players: a. Chytridiomycetes break down complex fibers. b. Cellulolytic bacteria break down cellulose. Requires branched-chain fatty acids, which are produced by amino acid fermenters c. Product of a and b is glucose. EMP and ED by a and b organisms take those to pyruvate. d. Pyruvate is fermented by various fermentative bacteria to short-chain fatty acids (e.g. acetate, lactate, propionate) e. H2 and CO2 are frequently produced. Used by methanogens to produce methane (syntrophy) f. The cow eats the short-chain fatty acids. Chapter 22 Biogeochemical cycles. For each, know the major players (more processes here like repiration ,lithotrophy, methanogenesis). A reservoir is the part of the biosphere that contains significant amounts of an element. Acts as both a source for that element for living organisms and as a sink to which it returns. A. Carbon cycle- Global reservoirs are atmosphere (small) and ocean. Land is the largest but is the least accessible. Carbon cycles between CO2 and various reduced forms of carbon, including biomass. Depending on the presence of O2, carbon cycling could be: a. Aerobic (ocean photic zone, oxygenated surfaces of terrestrial habitats) i. Photosynthesis fixes CO2 into biomass. Bacteria, Protists, Plants. Produces O2 and organic compounds ii. Lithoautotrophs also fix CO2 to biomass. Bacteria and Archaea. iii. Aerobic Respiration returns CO2 to atmosphere. b. Anaerobic (subsurface; Soil, benthos, rock). Lower rates of biomass production than aerobic i. Fermentation, anaerobic respiration with alternate electron acceptors, e.g. NO3 and SO4, and lithotrophs with inorganic electron donors, e.g reduced forms of S and N and alternate electron acceptors (no O2 here). ii. Major concern is methanogenesis. CH4 is a potent greenhouse gas. B. Water cycle- Water precipitates as rain; falls to earth. It is returned by evaporation to the air. BOD (how it happens, why bad). BOD decreased by WWT (wastewater treatment). Know the steps a. Preliminary- removes solid debris b. Primary- Find screens and sedimentation tans remove insoluble particles. Together with solid debris form sludge c. Secondary- Microbial decomposition of soluble organic content by aerobic respiration and methanogensis Primary versus secondary immune response Primary Antibody Response -Via disease (natural development of response) or vaccination (body doesn’t suffer disease) -Antibodies appear in serum after several days -B cells that bind antigen make antibodies -IgM, then to IgG (isotope switching) -Some B cells become memory cells, allowing a stronger response in the future Secondary Antibody Response -Via a second exposure to pathogen or booster dose -Antibodies appear in blood within hours -A much bigger response, with mostly IgG General antibody structure: IgG, IgA and IgM IgG = Y shaped -IgG = A monomer with four subclasses - Most abundant antibody in blood and tissue fluids - Opsonin; can cross placenta; activates complement -IgA = Most commonly found as a dimer - Secreted across mucosa - Abundant in secretions such as tears and breast milk -IgM = Monomer (on B cells) or pentamer - First antibody detected during an immune response Humoral immune response – requires 1) Antigen presenting cell (macrophage) – what is on its surface? MHC-II and antigen 2) T helper (TH2) cell – what is on its surface? CD4 and T cell receptor 3) B cell: -Clonal selection: selection of one type of B cell that is appropriate for making antibodies for that immunogen -Clonal expansion: replicate chosen B cell – Becomes one of what 2 cell types? Plasma cell: secreted antibodies coat extracellular antigens -Prevent virus binding to target cells Memory B cell: Reactivate if binds antigen again -Fast response—no need for TH2 binding -look like original B cell & are ready in case disease comes back in future How do antibodies protect us? a) Neutralize target b) Specific opsinization c) Direct complement killing Chapter 25 Koch’s Postulates: Criteria for establishing a causative link between an infectious agent and a disease 1. Microbe is always present in a diseased host a. Absent in healthy host b. Exception: helicobacter pylori- microbe may be present but only causes disease in some hosts 2. Microbe is grown in pure culture a. No other microbes present b. Exception: Can’t grow viruses or some microbes in pure culture 3. Introduce pure microbe into healthy host a. Individual becomes sick 4. Same microbe re-isolated from now-sick individual Virulence factors – a trait encoded genetically by a pathogen allowing the pathogen to cause disease 1. Virulence genes may be found on pathogenicity islands in the chromosome, on plasmids, or even on phage genomes a. Pathogenicity islands contain clusters of virulence genes with specific functions 2. Virulence is a measure of the severity of a disease Primary vs. Opportunistic pathogen 1. Primary- Cause disease in healthy hosts a. Aren’t usually in a healthy host 2. Opportunistic- cause disease only in immunocompromised patients Spread of infection: 1. Horizontal transmission: From on member of species to another a. Fomites- inanimate objects (used tissue) b. Vectors- transmitted by insect between animals (mosquito or tick) c. Direct- sneeze on someone d. Food- chef has salmonella, handles food, and gives to customer from eating food 2. Vertical transmission: a. From parent to child (HIV) 3. Accidental transmission: a host who is not part of the normal infectious cycle unintentionally encounters that cycle from a reservoir (limes disease in humans) What is a Reservoir? 1. An animal, bird, or insect that normally harbors the pathogen 2. Pathogens use portals of entry best suited to their mechanisms of pathogenesis a. Mouth: food-bourne pathogens (salmonella) b. Respiratory tract: airborne pathogens (influenza) Attachment: 1. Adhesin- the general term for any microbial factor that promotes attachment a. Important for colonization 2. Pili/fimbriae- hair like appendages used by bacteria to attach to a host’s cell surface a. Can specifically bind to certain tissues/cells 3. Afimbrial/non pilus adhesins- less complex, not specific a. Streptococus pyogenes: M protein b. Bordetella pertussis: Pertactin 4. Biofilm- when bacteria attach to surfaces in bulk a. Play important role in chronic infections Exotoxins: 1. Cell membrane disrupters: a. Alpha toxin i. Produced by Staphylococcus aureus ii. Forms a transmembrane, seven-member pore in target cell membranes iii. Cause red blood cells to lyse 2. Protein synthesis disrupters: a. Shiga toxin (AB toxin) b. Leads to cell death 3. Second messenger pathway disrupters: a. Stable toxin or Cholera toxin 4. Superantigens: a. Doesn’t bind where its supposed to; binds nonspecifically, stimulating tons of T cells (10%) i. Go into shock and experience systemic inflammation 1. Toxic shock syndrome 5. Proteases: a. Toxins that cleave host cell proteins and cause damage b. Anthrax toxin i. Made by Bacillus anthracis ii. Two active toxins: 1. Edema factor raises cAMP levels (fluid secretion, tissue swelling) 2. Lethal factor cleaves protein kinases (blocks immune system) Simple AB toxins: 1. B subunit- binds to host cell a. delivers A subunit to cytoplasm b. often five B subunits form a pore for A entry 2. A subunit- has toxic activity a. ADP-ribosyltransferase i. Diptheria toxin ii. Cholera toxin ADP-Ribosylating Toxins: 1. Diptheria toxin (simple AB toxin) a. targets protein synthesis b. Made by Corynebacterium diphtheriae) c. Ribosylates elongation factor 2 d. Blocks ribosome function; cell dies i. Forms pseudomembrane over trachea 2. Cholera toxin (AB5 Toxin) a. Targets second messenger signaling b. Made by Vibrio cholera c. Ribosylates to over activate adenylate cyclase d. cAMP activates ion transport; water follows i. uncontrollable diarrhea & dehydration -Ear infections & lungs (elderly) Mycobacterium tuberculosis: What are its most important virulence traits? -Mycolic acids -Waxy, produce T cells & result in inflammation -Grows very slowly Forms calcified tubercles in the lung (can go latent & reactivate) Gastrointestinal infections Rotavirus – the most common cause of childhood diarrhea & lethal dehydration -Causes gastroenteritis -Antibiotics ineffective on viruses -If kill competing bacteria, allows C. difficile to growàcauses gastrointestinal disease Salmonella typhimurium and Shigella dysenteriae: How do these organisms initiate infection? -Inject toxin via Type III secretion -Bacteria invade epithelial mucosa in GI tract What are their reservoirs? -Contaminated food and water (fecal contamination) Which one produced a toxin that inhibits protein synthesis? -Shigella can produce Shiga toxinà dysentery & kidney failure E. coli: Enterotoxogenic E. coli or ETEC: What are its most important virulence factors? -Adhesion factor via fimbriae; produces 2 exotoxins Genitourinary tract infections (know reservoirs) UPEC -Move against flow of urine & adhere via pili -Reservoir: humans; intestines Treponema pallidum: -Spirochete -Causes Syphilis -3 stages: -Primary syphilis: Chancre (sore) at sire of infection -Secondary syphilis: generalized rash -Tertiary syphilis: effects on heart & CNS -Difficult/impossible to treat because is autoimmune -Reservoir: humans; spread by direct/sexual contact Chlamydia trachomatis: What is an obligate intracellular pathogen? -A pathogen that cannot grow outside of a host cell What is special about the developmental life cycle of this pathogen? 1. Elementary bodies (infectious form, not active) bind and enter eukaryotic cell by phagocytosis 2. Elementary body differentiates into reticulate body 3. Reticulate bodies replicate 4. Reticulate bodies differentiate to elementary bodies and form inclusions 5. Elementary bodies are released Reservoir: Humans Neisseria gonorrhoeae: What are the most important virulence factors? -Adherence in genital tract Why will there probably never be a vaccine for this disease? -It is constantly changing its surface to make it seem non-foreign to immune system Reservoir: humans CNS infections (know reservoirs) Neisseria meningitidis: What are 2 most important virulence factors? -Has thick capsule and type IV pili Reservoir: humans Clostridium species produce toxins that can cause disease without infection Botulinum toxin -Anaerobe, grows in canned food -Endospores survive unless autoclaved -Toxin blocks release of acetylcholine -Causes flaccid paralysis Reservoir: canned food Tetanus toxin -Anaerobe, grows in puncture wounds -Blood flow interrupted; tissue becomes anaerobic -Toxin blocks release of GABA, inhibitory transmitter -Causes spastic paralysis (muscles clench & can’t release; death by suffication) -Reservoir: soil Sepsis (systemic infection) Yersinia pestis: Bubonic plague: Moves to lymph nodes Septicemic plague: Moves to bloodstream (groin bubos burstàbloodsteamàlungs) Pneumonic plague: inhaled (highly infectious) Reservoir: rodents Vector: rat flea Lyme disease: Borrelia burdorferi – spirochete 3 Stages: 1. A bull’s-eye rash; localized (erythema migrans) 2. Joint, muscle, and nerve pain 3. Arthritis, with WBC’s in the join fluid (autoimmune) Reservoir: White tailed deer, mouse Vector: ticks