BIOS 111 exam 1 study guide
BIOS 111 exam 1 study guide BIOS 111
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This 13 page Study Guide was uploaded by Sierra Mongeon on Tuesday February 2, 2016. The Study Guide belongs to BIOS 111 at University of Nebraska Lincoln taught by Dr. Kenneth Nickerson in Spring 2016. Since its upload, it has received 300 views. For similar materials see Microbiology in Biology at University of Nebraska Lincoln.
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Date Created: 02/02/16
1 MICROBIOLOGY EXAM 1 STUDY GUIDE Taxonomy ● 3 kingdoms of lifEukaryotes, Prokaryotes, Archaea Majority of Prokaryotes are bacteria all forms of life evolved from cells >3 billion years ago ● Eukarya: Animals, plants, algae, etc. ● Archaea:extreme halophiles, thermophiles, methanogens ● Prokarya: Bacteria ○ cyanobacteria (photosynthetic) ○ Gram + and Gram ○ Advantages of studying bacteria: grow large #s, rapid growth, single cells, genetic clones: same genetic i same basic biochemistry (amino acids, ATP) as other forms of life. ● “Molecular clock”16s ribosomal RNA (rRNA), helps us analyze the relatedness of all life ○ present in all cells ○ highly conserved (passed on through all forms of life as they evolved) ○ helped us develop the taxonomy system Carl Woese ● Eukaryotic organelles (mitochondria, chloroplasts) are derived from prokaryotic cells ○ have their own ribosomes, DNA Ribosomes ● site oprotein synthesis ○ protein is formed by copying DNA into mRNA (messenger), which travels to ribosome (made out of rRNAstructural component of ribosome). mRNA contains combinations of 3 nitrogen bases (codons), which code for one specific amino acid. The correct amino acids are brought to the cell by tRNA (transfer RNA) who translate the codons and attach amino acids together in a chain with peptide bonds (polypeptide chain). When a “stop” codon is reached, the chain is released and a protein is formed. ○ In short, DNA>RNA>ribosome>protein ● most amino acids are the Lform (there is also the Dform, which is rarer) ● prokaryotic ribosomes are 70s (smaller than 80s eukaryotic) ● use 90% of cell’s energy ● made of rRNA and protein ● bacterial ribosomes=target of many antibiotics (Abx) 2 History of Microbiology ● People did not think microbes existed prior to 1800s ● 18761906= Golden age of microbiology ● Ignaz Semmelweis 1847: found childbirth fever, a fatal disease among pregnant women, was spread through dirty hands of physicians (they didn’t wash hands between patients). Germs spread by shaking hands. When physicians washed hands, deaths fell from 10% to 1% ○ fomite: nonliving object that can spread infection. Ex: chair, cell phone etc. Microbes are on everything!! ○ Hospital Acquired (HA) infections= nosocomial ■ Major cause= poor hand washing, not washing equipment between patients (fomite) ● Louis Pasteur ○ proved microbes cause fermentation and produce ethanol/ make alcoholic drinks ○ proved microbes make milk to sour ■ pasteurization: killing microbes in a liquid by heating it ○ proved life can exist without air (anaerobic) ○ discovered concept of vaccines ■ heat bact. to destroy DNA plasmid for toxin ● Robert Koch father of medical microbiology ○ found B. anthraci in blood of dying animals, injected into healthy animals and they died too. ○ Koch’s postulates: ■ 1. Microorganisms (MO) found in sick individuals but not healthy ones ■ 2. Isolate MO from sick, grow in pure culture apart from host (prove MOs can live on their own) ■ 3. Inject healthy individual with the MOs grown in step 2, healthy host becomes sick ■ 4. Reisolate MO from newly sick, grow in culture, and see they are the same as the original ○ Exceptions to Koch’s postulates: viruses, bacteria that can’t grow in culture (leprosy)opportunistic pathogensMOs present in healthy individuals, but can cause disease if immunity becomes impaired.) Germ Theory of Disease ● We found which specific bacteria cause which disease! ● Proven by Koch’s postulates 3 Microscopy ● Culture techniques liquid, solid surface (agar gel) which can be sterilized, melted and repoured many times ● Clone=entire bacterial colony derived from a single cell (they all have exactly the same genes) ● Heat fixingkills microbes, makes them stick to slide so they can be stained ● Staining: coloring cells with a dye. Made of salts with both positive and negative ions ○ which ion is colored=chromophore. ■ Basic=positive ion ; Acidic= negative ion ■ Bacteria have negatively charged cell wall basic dyes used to stain actual bacteria, acidic dyes useegative staining\ ○ simple stai single basic dye in solution ○ Mordant=chemical added to soln. to intensify stain or to coat a structure (such as flagella) ● Differential staining:dyes react differently with different types of bacteria; used to distinguish and identify ○ Gram stain; Know the process and why it works! ● Special stains: ○ negative stain (used to see capsules) ○ flagella stain: thickens flagella so it can be seen ○ endospore staining: used to see spores ● Light microscopy (LM): uisible li to observe specimens ○ compound light microscope and parts ● Resolving power: why do electron microscopes have higher resolution than light microscopes? ● refractive index=ability of an object to bend light. We change this by using immersion oil (less refraction, can see more detail) ● Types of LM: ○ Bright field (what we use in lab) ○ Dark field ○ Phase contrast ○ Fluorescence mmunofluorescence= attaching fluorescent molecule to an antibody→ attaches to specimen ● Other types of microscopy; using sound waves or using tiny probes to see atomic detail ● Electron microscopy: ○ uses electrons to view specimens instead of visible light ○ What is the difference between SEM and TEM? (What do they “see”?”) 4 Bacterial morphology ● Coccus: sphere, resists drying ○ characterized by the way they stick together after dividing ■ diplo; pair, strepto; in a line (like beads on a necklace)= one plane of division ■ tetrad and sarcinae ■ staphlyo = cluster of grapes ● Bacillus: rod shaped ○ diplo, strepto ● Vibrio= comma shaped ● Spirillum= spiral, thick, rigid body. use flagella to move ● Spirochete= thin, flexible, use axial filaments to move ● Fusobacteria= long, spindle shape with pointed ends ○ causes tooth decay Bacterial Structures ● Fimbriae: short, straight and thin projections on bacterial surface ● polymerized proteins ○ Functions ■ attachment to other bacteria or to surfaces (important in forming biofilms) ● attachment allows disease! No attachment=no disease ■ identification (antigenic specificity) allows them to be recognized by macrophagesCranberry juiceprevents UTI’s in women; prevents attachment ○ biofilms= community of MOs encased in a selfproduced extracellular matrix. ■ can attach to abiotic (non living) or biotic (living) surfaces ■ 99% bacteria in nature found in biofilms ● Pili: long, only one or two, hollow protein tube ○ Functions: ■ DNA transfer (conjugation (sex) pili). Can transfer genes for Abx resistance or other desirable traits ■ motility ● twitching and gliding movement ● Capsules sticky polysaccharide coat, viewed only through negative staining ○ Functions: ■ attachment!! ■ protective ○ appearance of bacterial colony tells you if there is a capsule or not 5 ○ large radius compared to size of bacteria ○ serotype: variations within one species of bacteria. Vaccines only protect against most common serotype ■ S. pneumoniae example from class ○ info. for capsule synthesis comes from DNA ● Spores: very resistant forms of bacteria; like “seeds” or “hibernating” cells ○ vegetative cell runs out of nutrients → forms spore (sporulation) ■ Takes about 7 hours ○ ***can germinate(turn into a living (vegetative cell) when given the right conditions ■ spores don’t make toxins! The living cells do ○ dormant=no metabolism, can live for thousands of years ○ very very resistantneed autoclave to sterilize ○ ubiquitous= present everywhere ○ made by bacillus (aerobic) and clostridium (anaerobic) bacteria ○ spore coat and cortex very rigid → protection ○ contents of living cell dehydrated viewed through phase contrast microscope ○ Abx don’t work against spores! (They only kill living bacterial cells!) ● Flagella: the mechanism for motion (motility) ○ 3 parts: ■ filament: the long outer part, made of protein flagellin ■ hook ■ basal body: anchors flag. to cell. Composed of central axle and rings ● in Gram +, only one set of rings ● in Gram , two sets (outer and inner) ● sets of rings corresponds to # of membranes the bacteria have! ○ peritrichous = many flagella covering surface of cell ○ monotrichous= one flagella ○ polar = at one or both ends of cell ○ lophotrichous= tuft coming from one pole ○ amphitrichous = one at both poles ■ common in spirilla ○ move by rotation: basal body rotates like a propeller, clockwise or counterclockwise ■ “runs”= moves in one direction for period of time ■ “tumbles” = flagella rotates other way, abrupt stop and change in direction ○ Taxis= intentional motion toward favorable conditions or away from bad ones ■ chemotaxis → chemical environment ○ Swarming= bacteria with many (peritrichous) flagella can work together as a group to move very rapidly across a solid surface. 6 ○ Flagellar protein H antigen used to distinguish among serovars (variations within a species of bacteria) ● Nucleoid: single, long, continuous strand of DNA called the bacterial chromosome ● Plasmid: circular, double stranded DNA molecules, extrachromosomal (not part of chromosome). May be gained or lost without harming cell. ○ carry genes for Abx resistance, toxins etc. ○ can be transferred ○ Importance in virulence = often code for toxins ● Inclusions = reserve deposits of nutrients, accumulated when nutrients plentiful for use in hard times. . ○ metachromatic granules ; named because they stain red with blue dye. Reserves of phosphate. Characteristic C. diphtheriae ○ can be polysacc, lipids, etc. Bacterial Cell Walls Function: prevent cell from bursting when water pressure inside cell is greater than water pressure outside cell, protect plasma membrane and interior of cell ○ target of some Abx. If no cell wall, bact. ruptures → lysis Structure: peptidoglycan (PG), a disaccharide ( NAG, NAMboth related to glucose) attached by polypeptides ○ forms a lattice structure ○ alternating NAM and NAG form carbohydrate backbone, adjacent rows linked by polypeptides ■ tetrapeptide side chains = four amino acids attached to NAMs in backbone ■ parallel tetrapeptide chains linked by peptide crossbridges ● penicillin interferes with formation of these bridges, so cell wall is weak and cell bursts Atypical cell walls: some cells have no or very little cell wall material ● Mycoplasma= smallest bact. that can live independently of host cells ○ no cell walls ○ plasma membranes contain sterols ● Archaea = may lack or have unusual cell walls ○ no PG, but similar substance called pseudomurein ● AcidFast cell wall = high concentrations of mycolic acid (waxy lipid), forms a layer outside peptidoglycan. ○ hydrophobic, waxy cell walls, sticking and clumping Damage to cell walls ● lysozyme ○ destroys Gram + cell walls, remaining cellular contents = protoplast ○ Gram walls not completely destroyed, whats left = spheroplast 7 ○ Both protoplasts and spheroplasts burst in pure water d/t no cell wall, rapid inflow of water (osmotic lysis) ● Lforms = bacteria that can lose their cell walls and swell into odd shapes ● penicillin and similar Abx inhibit cell wall formation Plasma membrane ● encloses cytoplasm, is a bilayer (two layers) ○ phospholipids hydrophilic heads, hydrophobic tails. ○ Draw the structure of a phospholipid and how they form a bilayer. ● peripheral (outside, usually enzymes or for structural support) and integral proteins (embedded in. Transmembrane= span entire membrane) → fluid mosaic model = things can move around (as viscous as olive oil). Breaks and tears in membranes can heal themselves ● selectively permeable = only certain things in or out ○ lipid soluble, small, nonpolar molecules can easily pass.Water also passes easily ○ large, polar molecules don’t ● mesosomes = large, irregular folds in the membrane. Not true cell structures, created by preparing cell for EM ● can be destroyed by Abx→ no membrane, cell can’t live ○ also destroyed by alcohols, ammonia and other disinfectants Movement of materials across membranes (for more depth, see Ch. 4) ● simple and facilitated diffusion ○ moves according to their concentration gradient (high→ low) ○ facilitated = large molecules helped through by proteins ○ cell does not expend energy ● osmosis = net movement of water across a membrane ● osmotic pressure= pressure required to stop the flow of water ● isotonic, hypertonic, hypotonic: what do they mean and how do they apply to water movement? ● active transport movement of molecules against their concentration gradients, requires cellular energy. Usually movement from inside to outside of cell ○ group translocation = substance is chemically altered during transport, once it is inside cell it is changed back so it is impermeable and remains in the cell 8 Phagocytosis ● function of macrophages (human body immune cells) ● “eating” foreign things ○ engulfing and killing (digesting) ● Phases: ○ chemotaxis: chemical signal of infection, macrophage moves to it ○ adherence: binds to and recognizes bacteria by PAMPS ■ PAMP= pathogen associated molecular patterns ■ common PAMPs are fimbriae, flagella and cell walls (but you have to be able to “see” the surface; not possible if there is a capsule, this is why encapsulated bacteria cause disease.) ○ ingestion= taking in, engulfing ○ digestion= by lysosome with digestive enzymes inside macrophage ● antibodies= specialized proteins that bind to receptors on bacteria, which allow macrophage to find and eat it Prokaryote vs. Eukaryote Table in Chapter 4 of text and was presented in class. Know the basic structures of each. Key points: Prokaryotes Eukaryotes ● no nucleus ● the opposite of what’s on prokaryotes ● flagella is a seperate structure from side (nucleus, flagella, size, sexual cell (aka not contained in cell DNA recomb.) membrane but attached to outside) ● 80S ribosomes ● cell wall= complex, peptidoglycan ● cell walls= simple (chitin or cellulose) ● 70S ribosomes ● reproduce by binary fissionno sexual DNA recombination ● smaller than Euk. cells (about .22 microns) 9 Gram + vs Gram – Table 4.1 What are the differences between the two? How do we tell them apart Gram + Gram ● one cell membrane ● two cell membranes, inner and outer ● thick peptidoglycan layer ○ outer= periplasm ● teichoic acids negatively charged ● thin peptidoglycan (PG) layer ○ regulate movement of cations between the two membranes, more (+ charged) susceptible to mechanical breakage ○ role in cell growth ● no teichoic acids ○ provide antigenic specificity ● outer membrane= high conc. of ■ specific identification transport proteins and enzymes. ■ allows them to be ○ consists of grouped with other lipopolysaccharides (LPS), medically significant lipoproteins and phospholipids types ○ strong negative charge ● 2 rings in basal body (one set) important in evading ● exotoxins only phagocytosis ● high resistance to mechanical ○ barrier to Abx, detergents, stress/disruption (d/t thick cell wall) dyes, metals, bile etc. ● resistant to drying ○ important molecules come in through porins ● LPS= 3 components: lipid A, core polysaccharide, O polysac. ○ Lipid A = endotoxin, causes illness ○ Core polysac= structure/stability ○ O polysac = antigen, I.Ding ● 4 rings in basal body (2 sets) ● prod. both endo and exotoxins ● not resistant to drying out How does Gram staining work?? ● Crystal violet stains both types, mordant forms large crystals of dye, alcohol dries PG of Gram+ but dissolves the periplasm and PG layer of Gram cells and violet comes out. Counterstain safranin absorbed by both, but violet masks it so only Gram bacteria are pink ● Doesn’t always work ○ Some bacteria are Gram variable, old/dead specimens wont stain correctly ○ Variation within the same species 10 Diseases of the Day (DOD): Tooth Decay ● caused by biofilm on teeth a. mutans ● anaerobic bacteria on tooth surface=fermentation=acid, which dissolves enamel of tooth ○ air you breathe doesn’t reach the surface bacteria because there are many layers of different bacteria on tooth surface ○ they are also encapsulated; helps them stick, prevents oxygen from reaching ○ cariogenic=cause dental caries ● sucrose= disaccharide in common table sugar; is used by bacteria to make dextran, which is a capsule component, very easily ● xylitol = sugar alcohol in some chewing gum may prevent tooth decay Tetanus ● caused by lostridium tetspores getting into body and germinating into living cells ○ anaerobic cell get into areas of body where no oxygen, like under skin ■ can get tetanus from wounds (esp. puncture wounds) most common ■ also from dirty needles, piercings, abortion, and circumcision ○ bacteria commonly found in soil ○ exotoxin= toxin formed inside cell and excreted outside of cell ○ causes uncontrollable muscle contraction toxin tetanospasmin ■ tetanus commonly called “lockjaw” ■ you die of exhaustion muscles can’t stop contracting ○ **vaccine= toxin purified and then deactivated with formaldehyde, turning it into toxoid** ■ This is a common way vaccines are made from toxin producing bacteria!! ■ need booster every 10 years or if wounded ■ body recognizes toxoid, so if you get infected, your body automatically recognizes it and attacks it (immunity) Botulism ● Caused by Clostridium botulinspores ○ C. botulinuis an obligate anaerobe, like tetanus ● Can get it through wounds or food ○ don’t feed infants honey!!= spores, infants have less stomach acids and fewer competing MOs in digestive system, can get botulism ○ botulism means “meat” spread through meat industry ○ Canning industry perfect environment to grow! (anaerobic and tons of food!), so food industry has very effective methods to kill spores (pH, high temp, use of preservatives) ■ the danger lies in home canning food you can make mistakes (not heat long or hot enough to kill spores) ● Produces protein exotoxin 11 ● Flaccid paralysis (opposite of tetanus) inability to contract muscles (limp), eventually diaphragm fails and you can’t breathe→ suffocation ○ other symptoms: can’t hold head up, vision problems, can’t swallow ● Types A, B, E most common ○ Type A used in Botox= small injection to paralyze facial muscles, reducing wrinkles ○ 7 different neurotoxins produced by botulism bacteria ● Botulism toxin= most potent, 1 million times stronger than cyanide ● Small amts. toxin can be used to treat some diseass (like parkinson’s) where there is too much muscle contraction Anthrax ● Bacillus anthraciGram +, sporeformer, large bacteria, aerobic ○ discovered as cause of anthrax by Koch in 1876 (koch’s postulates) ● spores commonly used in bioterrorism/ biological warfare 2001, sent in US mail to government officials, 5 died ○ U.S. soldiers entering Iraq vaccinated with AVA anthrax vaccine absorbed ■ toxin is deactivated with formaldehyde = toxoid ■ body recognizes toxoid → immunity ○ Anthrax used in Iraq by Saddam Hussein, Japanese in WWII against China (put in balloons to try and send it overseas to America) ○ Fort Detrick bioterror microbiology studied in U.S To protect against it, we have to understand the organisms! ○ Gruinard Island quarantined, no humans allowed, covered in anthrax ○ Recent Omaha study, B. globigused to determine effects of wind on spore spreading ● primarily a disease of animals → zoonosis; esp. grazing animals (grass ea ing) ○ B. anthraci found in soil ○ spores = longevity and resistance!! ■ “anthrax fields” : many animals die of anthrax, decompose, bact. from their body forms spores that live in soil ● Burning dead animals prevents sporulation ● 3 modes of entry: ○ Skin (cutaneous); most common ■ enters through wounds ■ ID (infectious dose) 1050 spores ○ Pulmonary (breathed in) ■ ID 15000 ○ GI tract (eating) ■ ID 1 million ● spore germinates, macrophages unable to kill (capsulemade of amino acids, not polysaccharide = unusual!) ● spreads to lymph nodes and into blood, vegetative cells multiply and release toxin 12 ○ septicemia = microbial growth in blood, death if untreated ● Abx : penicillin, ciprofloxin etc. ● 2 plasmids: capsule and toxin ○ Louis Pasteur 1881 vaccine for sheep ■ high temp destroy plasmid that codes for toxin ○ Importance of plasmids and vaccination: ■ B. cereus common and harmless soil bacteria ■ 1 plasmid (for one kind of toxi. thuringiens= toxic to insects ■ 2 plasmids (capsules and toxin). anthracis ● lose 1 plasmid, bact. not dangerous!! ● spores from these 3 bact. look and test alike ● Diagnostics: sample cultured on blood agar plate, if grey nonhemolytic samples found, sample is sent to CDC (center for disease control) ○ they do fluorescent antibody tests, bacteriophage and PCR tests ■ PCR very fast, finds gene, polymerase chain reaction Diphtheria ● Caused by orynebacterium diphtheri Gram +, no spores, nonmotile, resists drying, obligate aerobe (needs oxygen) ○ contains characteristic metachromatic granules (polyphosphate granules) ● Diphtheria = “leather”, forms tough grey membrane containing dead cells, fibrin (from host) and bacterial cells ● Transmitted through air ○ gets into throat, colonizes, body’s inflammatory response causes throat to swell shut = strangulation ○ common killer of children → smaller throats ■ 90% mortality in child factories during industrial revolution = epidemic ■ main reason for child labor laws (more crowding = easier to spread disease) ● pleomorphic (more than one shape) club or vshaped ● produces two part exotoxin AB toxin ○ A part = toxic ; B part = helps A part get into host cell ■ B (binding part) attaches to host cell, entire toxin enters cell, A part inhibits protein synthesis by modifying ribosomes, host cell dies ■ 10 micrograms toxin = kill a human ■ toxin doesn’t bind to rat or mouse cells, does bind to human and rabbit ○ gene for toxin can be turned on or off ■ high iron = no toxin, bacteria is happy ■ low iron = toxin produced, gene turned “on” ● Vaccine ○ purify toxin, deactivate with formaldehyde (how most exotoxin vaccines are maide) forming toxoid which can be killed/ recognized by macrophages 13 ○ 1926 mass immunization in U.S with DPT (diphtheria, pertussis, tetanus) ○ Vaccines don’t work if you don’t use them! ■ Russia stopped vaccinating, disease is coming back as a big problem (emerging) ○ if infected, penicillin and antitoxin ← in emergency ○ Today, use DTaP vaccine, need booster every 10 years Review of general chemistry….see previously posted notes for a comprehensive review of this topic
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