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BSC 310 Week 1 & 2 Notes

by: Caitlin Owens

BSC 310 Week 1 & 2 Notes BSC 310

Caitlin Owens
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This includes the notes from lecture, a brief book outline, and homework from chapter 1 & 2.
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This 16 page Class Notes was uploaded by Caitlin Owens on Friday January 29, 2016. The Class Notes belongs to BSC 310 at University of Alabama - Tuscaloosa taught by in Spring 2016. Since its upload, it has received 37 views. For similar materials see Microbiology in Biology at University of Alabama - Tuscaloosa.


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Date Created: 01/29/16
Microbiology Lecture 1 {1/14} MICROBIOLOGY- study of microorganisms MICROORGANISMS- all single-celled, microscopic organisms plus viruses, which are microscopic but not cellular Microbiology revolves around 2 themes: 1. Understanding basic life processes a. Microbes are excellent models for understanding cellular processes in unicellular and multicellular organisms 2. Applying that knowledge to the benefit of humans a. Microbes play important roles in medicine, industry, and agriculture Importance of Microorganisms: -Oldest form of life, largest mass of living material on Earth, carry out major processes for biogeochemical cycles, can live in places unsuitable for other organisms, all other life forms require microbes to survive Microbial Cell Structure: -Eukaryote: contains nucleus and subcellular organelles -Prokaryote: no nucleus (does have nucleoid), can have cell wall and membrane, bacteria and archaea Properties of ALL Cells: 1. Metabolism- cells take up nutrients, transform them, and expel wastes a. Genetic (replication, transcription, translation) b. Catalytic (energy, biosynthesis) 2. Growth-nutrients from the environment are converted into new cell materials to form new cells 3. Evolution-cells evolve to display new properties, phylogenetic trees capture evolutionary relationships Properties of SOME Cells: 1. Differentiation-some cells can form a new cell structure such as a spore 2. Communication-cells interact with each other by chemical messengers 3. Genetic Exchange-cells can exchange genes by several mechanisms 4. Motility-some cells are capable of self propulsion Microorganisms & their environments: -They live anywhere there is lifeà biosphere (100-150 km into earth, 121°C) *Populations, Communities, Ecosystems -Diversity and abundances of microbes are controlled by resources and environmental conditions(ex. temp, pH, O2, chemical & physical) -The activities of microbial communities can, in turn, control the chemical and physical properties of their habitat Impact of Microorganisms on Humans: -Control key ecosystem functions -Agents of disease -Key components of agricultural systems -Key roles within food industry-expanding to “biotech” Microbiology began with the invention of the microscope… -Hooke:1664, discovered fungi -van Leeuwenhoek: discovered bacteria -Cohn(discovered endospores & cotton stoppers), Pasteur, Koch: +~150 years -Hesse (agar…jelly) -Petri (dish) Pasteur -wine industry -optical isomers -defeat of spontaneous generation -rabies vaccine (Jenner smallpox 1 )t -swan-neck flask experiment Koch -solid media, pure culture -Koch’s postulates-isolation of Microbacterium tuberculosis Beijerinck & Winogradsky +~50 years Beijerinck: enrichment culture-allows development of pure culture of many environmental microorganisms; first to hint at presence of viruses Winogradsky: chemolithotrophy, nitrogen fixation Modern Era +~60 years -DNA as informational molecule of life Microbiol ogy Lecture 2 {1/19} Light Microscope RESOLUTION: the ability to distinguish 2 adjacent objects as separate and distinct; limit of resolution for light microscope is about 0.2 micrometers; limits effective magnification to about 2000x -bright field-works great for pigmented cells but most bacteria are very difficult to see -staining can be used to increase contrast *simple stains, differential stains, specialty stains, gram stain most common -fluorescence microscopy-UV light source and many times (but not always) fluorescence stains -differential interference contrast -Confocal Scanning Laser Microscopy *couples a computerized microscope, laser light soutce and fluorescent dye including green fluorescent protein Electron Microscope -use electrons instead of photons to image cells and structures-improves resolution from 0.2 micrometers to 0.2 nanometers -Transmission Electron Microscopy (TEM) *electromagnets function as lenses *system operates in a vacuum *enables visualization of structures at the moleculat level *specimen must be very thin (20-60nm) and be stained -Scanning Electron Microscopy (SEM) *specimen is coated with a thin film of heavy metal (ex. gold) *an electron beam scans the object *scattered electrons are collected by a detector and an image is produced *even very large specimens can be observed, magnification range of 15x- 100,000x Cell Morphologies -coccus, rod, spirilium, spirochete, budding & appendaged bacteria, filamentous bacteria (know sizes ****) -bacteria range in size -two giants-epulopiscium fishelsoni, thiomargarita namibiensis -impact of size *the higher surface area to volume ratio, the faster diffusion can deliver/ remove compounds *it is calculated that a cell must have a volume of atleast 0.002 microliters^3 (sphere 0.15 microliter in diameter) to contain the necessary proteins, DNA, ribosomes, etc. to function Membrane Structure -phospholipids form the basic unit of the cytoplasmic membrane -fluid mosaic model-hydrophilic and hydrophobic groups -membrane proteins Microbiology Lecture 3 {1/21} Archaeal phospholipids-isoprene units Archaeal membranes-can be monolayer or bilayer Membrane Function *permeability barrier- prevents leakage and functions as a gateway for transport of nutrients into, and wastes out of the cell *protein anchor-site of many proteins that participate in transport, bioenergetics, and chemotaxis *energy conservation-site of generation and use of the proton motive force -water>glycerol>tryptophan>glucose>Cl->K+>Na+ for permeability -How do cells acquire compounds with low permeability or against a concentration gradient? Transporters Transport Systems -3 major classes of transport systems in prokaryotes 1. simple transport-driven by the energy in the proton motive force 2. group translocation-chemical modification of the transported substance driven by phosphoenolpyruvate 3. ABC system-periplasmic binding proteins are involved and energy comes from ATP *all require energy in some form, usually proton motive force for active transport -3 transport events are possible 1. uniport-transport a single molecule across the membrane 2. symport- function as co-transporters 3. antiport-one molecule transports in and one molecule transports out Simple Transport -well studied-lac permease of Escherichia -lactose is transported into E.coli by the simple transporter lac permease, a symporter (H+) *activity of lac permease is energy driven (proton motive force) -although referred to as “simple”, these should not be considered a simple tube as substrate interacts with protein, conformational changes are associated with transport, and the system is subject to regulation Group Translocation -best studied system-phosphotransferase system in E.coli *moves glucose, fructose, and mannose *5 proteins required *energy derived from phosphoenolpyruvate ABC (ATP Binding Cassette) System ->200 different systems identified in prokaryotes -often involved in uptake of organic compounds (sugars, amino acids), inorganic nutrients(sulfate, phosphate), and trace metals -typically display high substrate specificity -contain periplasmic binding proteins-specific to gram-negative bacteria-or anchored binding proteins (gram-positive bacteria) -in gram-positive bacteria substrate binding protein is anchored to the exterior of the membrane Peptidoglycan -active transport of solutes generates significant osmotic pressure on call membrane (30PSI)- peptidoglycan is the rigid layer of the cell wall that resists this pressure -peptidoglycan is a polysaccharide composed of N-acetylglucosamine and N- acetylmuramic acid and amino acid (some D’s{should be L amino acid} and Lysine or diaminopimelic acid) -cell walls of gram-positive and gram-negative bacteria differ in structure Gram-positive bacterial cell wall & membrane -presence of teichoic acid and lipoteichoic acids(anchor wall and membrane together, lipids in the membrane)-composed of ribitol-allows bacteria to have slightly negative charge on its exterior Gram-negative cell wall & membrane -polysaccharide backbone -more complex -outer membrane outside of the peptidoglycan wall-lipopolysaccharides extending from outer membrane-can cause toxic shock in humans -contains porins for transport, ~1500 daltons can pass through (one AA~100D) -cytoplasmic membraneàpeptidoglycan wallàouter membrane -lipopolysaccaride (LPS) structure- O-specific polysaccharide, core polysaccharide, lipid A Archaea Cell Walls -S-layers *most common cell wall type among archaea *consist of protein or glycoprotein *paracrystalline structure (also found in bacteria) *no peptidoglycan-some contain pseudomurein (murein is a pseudonym for peptidoglycan) Prokaryotes without cell walls: Mycoplasmas(pathogenic bacteria), Thermoplasma(species of Archaea) Cell Surface Structures -capsules and slime layers (capsules exclude particles) *polysaccharide/protein layer *may be thick, thin, rigid, flexible *assist in attachment to surfaces-biofilms *protect against phagocytosis *resist desiccation -fimbriae *filamentous protein structures *enable organisms to stick to surfaces or each other -pili *filamentous protein structures *typically larger than fimbriae *assist in surface attachment *facilitate genetic exchange between cells (conjugation) *type IV pili involved in twitching motility and for some pathogens virulence Microbiology Lecture 4 {1/25} Cell Inclusions -carbon storage polymers *Poly-β-hydroxybutyric acid (PHB) àone of the research areas of my lab is to produce PHB from plant waste and then react with ethanol to produce a second generation liquid biofuel *glycogen-glucose polymer -inorganic phosphate storage-polyphosphates -elemental sulfur storage-sulfur globules -magnetic storage inclusions-magnetosomes Endospores -a bit of a misnomer to call this an “inclusion”-a cell within a cell -highly differentiated cells resistant to heat, harsh chemicals, and radiation -“dormant” stage of bacterial life cycle, ideal for dispersal via wind, water, or animal gut -only present in some gram-positive bacteria -structurally complex- exosporiumàspore coatàcore wallàcortex -dewatered, lower pH, quaternary structure of DNA changed -contains dipicolinic acid, small acid-soluble proteins (SASPs) -enriched in Ca2+ -longevity is easily hundreds of years *spore-forming bacteria grown from 750 million year-old glacier ice and 38-41 million years old in salts (oceans), also 20-30 million years ago in insects that have been fossilized by amber -may be able to grow in ice and salt, must repair DNA or have multiple copies of genomes Gas Vesicles -confer buoyancy in planktonic cells -spindle-shaped, gas-filled structures made of protein -gas vesicles impermeable to water Flagellum -different structure for gram-negative and gram-positive -have rotor and stator -Archaea also show flagella, although proteins are different from those observed in Bacteria and they are driven by ATP Gliding -a variety of Bacteria show gliding motility-slim *common in cyanobacteria-Oscillatoria (ex. pringle can) *non-gliding mutant- Flavobacterium -outer membrane is free to move-transmembrane protein works like a ratchet with glide proteins to move membrane Microbial Taxis TAXIS-directed movement in response to chemical or physical gradients -chemotaxis: response to chemicals -phototaxis: response to light -aerotaxis: response to oxygen -osmotaxis: response to ionic strength -hydrotaxis: response to water How Chemotaxis Works -cell surface receptor senses compound, measures gradients in time (not space) -complex molecular machinery measure the rate of “hits” -cells alternately “run” and “tumble” *if rate of contact continues to increase runs become longer *if rate of contact decreases, runs become shorter *tumbles “pick” a new direction at random -if no attractant present-random movement; attractant present-directed movement EUKARYA-a domain of life characterized by celss containing a membrane- enclosed nucleus and other subcellular organelles including mitochondria, Golgi complex, and endoplasmic reticula (no longer microtubules and microfilaments) -cell structure *NUCLEUS-membrane bound region containing chromosomes, visible under light microscope without staining, enclosed by 2 membranes, DNA is wound around histones (not for Bacteria but some Archaea), within the nucleolus-site of ribosomal RNA synthesis Nucleus & Cell Division -unlike Bacteria and Archaea, most Eukarya have 2 copies of each chromosome(diploid) -many microbial eukaryotes can be either diploid or haploid and may or may not show sexual reproduction -the presence of more than one chromosome and the presence of 2 copies of each requires special forms of cell division -vegetative cell division is called mitosis in Eukarya -chromosomes are replicated and partitioned into 2 nuclei-results in 2 diploid daughter cells -further specialization is required for sexual reproductionàMeiosis *reduces diploid number to the haploid number *results in four haploid gametes – upon gamete (2) fusion return to diploid state *cell-cell fusion rarely seen in Bacteria; likely evolved in Archaea Mitochodria, Hydrogenosomes, & Chloroplast -all specialize in energy metabolism -mitochondria-respirationa and oxidative phosphorylation -hydrogenosomes-anaerobic respiration-conversion of pyruvate to acetate, CO2 and H2 -chloroplasts-conversion of light energy to ATP and fixation of carbon -chloroplasts, mitochondria* and hydrogenosomes* suggested as descendants of ancient prokaryotic cells (endosymbiosis); *single origin *evidence that supports idea of endosymbiosis -mitochondria and chloroplasts contain DNA -DNA is circular -mitochondria and chloroplasts contain own ribosomes -ribosome sequences align with those of living bacteria Eukaryotic Mitochondria -bacterial dimensions (rod or spherical), single circular DNA molecule, 70S ribosomes -a few per yeast cell to over 1,000 in an animal cell -surrounded by two membranes, folded internal membranes called cristae -contain enzymes needed for respiration and ATP production Eukaryotic Hydeogenosomes -similar size to mitochondria; lack TCA cycle, enzymes, and cristae -oxidation of pyruvate to H2, CO2, and acetate -found in various anaerobic protists and some parasitic forms Eukaryotic Chloroplasts -chlorophyll-containing organelle found in phototrophic eukaryotes -size, shape, and number of chloroplasts vary -flattened membrane discs are thylakoids -lumen of the chloroplast is called the stroma, which contains large amounts of RubisCO (key enzyme in Calvin cycle) Other Major Eukaryotic Cell Structures -internal membranes, tubes and fibers, also present in Lokiarchaeota (Lokiarchaeota contain 17 of 21 signature eukaryotic proteins) -internal membranes *endoplasmic reticulum (ER): two types of ER (smooth and rough), rough contains attached ribosomes; smooth does not *golgi complex: stacks of membrane distinct from, but functioning in concert with, the ER, modifies products of the ER destined for secretion *lysosomes and other vacuoles *internal tubes and fibers: microtubules (25nm in diameter, composed of α- and β-tubulin; function in maintaining cell shape, in motility, in chromosome movement, and in movement of organelles), microfilaments (7 nm in diameter; polymers of actin; function in maintaining cell shape, motility by pseudopodia, and cell division), Intermediate filaments (8–12 nm in diameter; keratin proteins; function in maintaining cell shape and positioning of organelles in cell) Flagella & Cilia -confer swimming motility -cilia are shorter than flagella -structurally distinct from prokaryotic flagella -bundle of 9 pairs of microtubules surrounding the central pair -in cilia/flagella dynein is attached to the microtubules and uses ATP causing tubules to slide past one another -propel the cell using a rowing or whiplike motion Microbiology Lecture 5 {1/28} Essential elements as a percent of dry cell weight: C 50%, O 17%, N 13%, H 8.2%, P 2.5%, S 1.8% Trace elements: Boron, Cobalt, Copper, Iron, Manganese, Molybdenum, Nickel, Selenium, Tungsten, Vanadium, Zinc Macromolecular composition of a cell: Protein 55%, Lipid 9.1%, Polysaccharide 5%, Lipopolysaccharide 3.4%, DNA 3.1%, RNA 20.5% NUTRIENTS-elements and compounds required by cells for growth (form matters) MACRONUTRIENTS- nutrients required in large amounts (>1% dry cell mass) MICRONUTRIENTS-nutrients required in trace amounts (<1% dry cell mass) Carbon -required by ALL cells -typical bacterial cell is ~50% carbon by dry weight -major element in ALL classes of macromolecules (same true for oxygen and hydrogen) -heterotrophs require organic carbon, autotrophs use carbon dioxide Nitrogen (N)-typical bacterial cell is ~13% nitrogen by dry weight; key element in proteins, nucleic acids, and many more cell constituents Phosphorus(P)-synthesis of nucleotides, nucleic acids, and phospholipids Sulfur (S)-sulfur-containing amino acids (cysteine and methionine); vitamins like thiamine, biotin, and coenzyme A Potassium (K)-required by enzymes for activity Magnesium (Mg)-stabilizes ribosomes, membranes, and nucleic acids; also required for many enzymes Calcium (Ca)- helps stabilize cell walls in microbes, plays key role in heat stability of endospores Sodium (Na)-required by some microbes Iron (Fe)-key component of cytochromes and FeS proteins involved in electron transport Growth factors-organic compounds required in small amounts by certain organisms-vitamins, amino acids, purines, pyrimidines Vitamins-most commonly required growth factors, most function as coenzymes Laboratory Culture od Microorganisms -culture media-nutrient solutions used to grow microns in the laboratory -2 broad classes 1. defined media-precise chemical composition is known 2. complex media-composed of digests of chemically undefined substances (ex. yeast and meat extracts) -liquid: cells grown in test tube or flask (mainly time shaken) -solid: are prepared by addition of gelling agent (agar or gelatin)-cells from colonies-typically easier to detect contaminants -selective media: contain compounds that selectively inhibit growth of some microbes but not others -differential media: contain an indicator, usually a dye, that detects particular chemical reactions occurring during growth -pure culture:culture containing only a single kind of microbe -contaminants: unwanted organisms in a culture -microbes are everywhere-sterilization of media is critical, aseptic technique should be followed Microorganisms grouped into energy classesàChemotrophs & Phototrophs -Preformed organic carbon-heterotrophs -CO2-autotrophs-RubisCo-key enzyme in cycle that fixes CO2 -Chemoorganotrophs: uses O2-aerobe -Chemolithotrophs:doesn’t use O2-anaerobe -Phototrophs: produces O2-oxygenic; doesn’t produce O2-anoxygenic Bioenergetics -Energy available in any reaction allows us to predict 2 things: 1. will a metabolic reaction occur 2. where/when will a metabolic reaction ovvur -free energy (G) is the energy released that is available to do work -change in free energy during a reaction is referred to as delta G^o (indicates standard conditions) -reactions with a negative delta G release free energy and are said to be exergonic -reactions with positive delta G require energy and are said to be endergonic - -free energy formation of Hydrogen gas and Oxygen gas is 0 -for the reaction A+BàC+D * Chapter 1 Homework -Characteristics of Achaea, Bacteria, Fungi, and Viruses *Bacteria-have cell walls that contain peptidoglycan; derive nutrients from organic or inorganic sources or conduct photosynthesis *Archaea-not typically associated with human disease; found in extreme environments *Fungi-eukaryotic, can be unicellular or multicellular *Viruses-can be seen only with an electron microscope; cannot survive outside a host cell - One of the first set of experiments to refute spontaneous generation was done in 1688 by Francesco Redi. Which of the following statements regarding Francesco Redi’s experiments is true? The results of his experiment demonstrated that living organisms are derived from other living organisms. -In 1861, Pasteur conducted his now-famous experiments using flasks with long necks bent into an S-shape. Imagine that you are a scientist working in Pasteur’s lab at this time. You decide to tip the flasks so that broth enters the long S- shaped neck. You then return the flask to its upright position. Predict the most likely outcome of tipping one of Pasteur’s S-necked flasks. The broth would become contaminated with microbes because they were trapped in the neck. -Metabolism is a unifying characteristic of all cellular organisms. Chapter 2 Homework -A student observed a stained specimen of bacteria using bright-field microscopy. At 100x magnification, there appeared to be only one cell in the field of view, but at 1000x it was clear that there were two cells close together. The ability to distinguish these two cells as separate entities is called resolution. -If a cell has a high surface-to-volume ratio, there will be enough surface area to get the needed nutrients in to support cellular metabolism and the accumulated waste out. -If an E. coli cell has a surface area-to-volume (S/V) ratio of 4.5, and a Pelagibacter ubique has an S/V ratio of 22, which cell will be able to exchange nutrients and wastes with the environment more efficiently? Pelagibacter ubique, because its cells are smaller Chapter 1 Book Outline GENOME-living blueprint of an organism; characteristics, activities, and survival of cell is governed by this PLASMID-small circles of DNA in prokaryotes that typically contain genes that confer a special property on the cell -Earth is 4.6byo and microbial cells first appeared 3.8-3.9bya-all cells have descended from a common ancestral cell [Earth’s atmosphere only contained N2 and CO2 for 2by, only anaerobic microorganisms could survive, phototrophic microorganisms evolved harvesting energy from sunlight, cyanobacteria(oxygen-evolving phototrophs) began the process of oxygenating earth’s atmosphere for multicellular organisms to evolve ECOSYSTEM-all of the living organisms, together with the physical and chemical components of their environment EXTREMOPHILES- large group of Archaea and Bacteria, whose collective properties define the physiochemical limits of life; live in extreme environments -History [Hooke-illustrates structures of molds [Van Leeuwenhoek-constructed simple microscopes, first to see bacteria [Cohn-studied unicellular algae which led him to bacteria, discovered endospores, use of cotton for closing flasks and tubes [Koch-infectious disease, agar plates, tuberculosis, postulates 1.suspected pathogen must be present in all cases of the disease and absent from the healthy animals 2. suspected pathogen must be grown in pure culture 3. cells from pure culture of the suspected pathogen must cause disease in a healthy animal 4. suspected pathogen must be reisolated and shown to to be the same as the original [Pasteur-spontaneous generation, Pasteur flask, vaccines for cholera/anthrax/rabies [Petri-“petri” dish-standard tool for obtaining pure cultures [Beijerinck-enrichment culture technique- microorganisms isolated from natural samples using highly selective nutrient and incubation conditions [Winogradsky-proposed concept of chemolithotrophy- oxidation of inorganic compounds to yield energy Chapter 2 Book Outline -Microscopes [Compound light microscope: bright-field, phase-contrast, differential interference contrast, dark-field, fluorescence [Gram stain: gram-positive bacteria appear purple, gram-negative bacteria appear pink because of differences in cell wall [Phase & dark-contrast improve image of unstained cells [Differential interference contrast employs a polarizer in the condenser to produce polarized light; cellular structures appear more 3D [Confocal scanning laser microscope-couples a laser to a fluorescent microscope, useful for viewing thick specimens [Transmission electron microscope-used to examine cells at very high magnification and resolution, only a thin section viewed [Scanning electron microscope-3D imaging of cells, specimen coated with a thin film of heavy metal, electron beam then scans across, only surface is typically visualized -Membranes [The lipids of Bacteria and Eukarya use ester linkages to bond fatty acids to glycerol, the lipids of Archaea contain ether bonds between glycerol and their hydrophobic side chains [Archaeal lipids lack fatty acids, hydrophobic side chains play the same functional role as fatty acids, formed from multiple units of the 5-carbon hydrocarbon isoprene [Cytoplasmic membrane of Archaea is formed from either glycerol diethers-20-carbon side chains, or diglycerol tetraethers-40-carbon side chains [Lipid monolayer membranes are extremely resistant to heat and are widely distributed among hyperthermophilic Archaea [Membrane is a permeability barrier and an anchor for many proteins -Characteristics of transport systems: 1. saturation effect- if concentration of substrate is high enough to saturate the transporter, which often occurs at very low substrate concentrations, the rate of uptake becomes maximal and the addition of more substrate does not increase the rate-this feature is essential for concentrating nutrients from very dilute environments 2. high specificity- many transport proteins carry only a single kind of molecule, whereas a few carry a related class of molecules 3. highly regulated-specific complement of transporters present in cytoplasmic membrane of a cell is a function of both the nature and concentration of resources in its environment


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