Microbiology Exam 1 Study Guide: Introduction & Visualization, Study notes of Microbiology

Download Microbiology Exam 1 Study Guide: Introduction & Visualization and more Study notes Microbiology in PDF only on Docsity!

Fungi Cellular Microbiology Exam 1 SG CHAPTER 1: INTRO TO MICROBIOLOGY Overview of Microorganisms

• Importance o Most populous & diverse group of organisms o Found everywhere on the planet o Role in recycling of essential elements o Source of nutrients & some carry out photosynthesis o Benefit society ▪ Food production ▪ Beverages ▪ Antibiotics ▪ Vitamins o Some are disease-causing in people, plants, or animals
• Characteristics o Generally < 1mm & too small to be seen with the naked eye o Simple in construction ▪ Lack differentiated tissues ▪ Unicellular (typically)
• Divisions o ▪ - Yeast : unicellular - Molds & mushrooms : multicellular ▪ Protists - Algae : photosynthetic - Protozoa : may be motile, hunters & grazers - Slime molds : 2 life cycle stages - Water molds : devastating disease in plants ▪ Bacteria - Don’t reproduce sexually - Referred to as “strains” = descendants of a single, pure microbial culture ▪ Archaea - Don’t reproduce sexually - Referred to as “strains” = descendants of a single, pure microbial culture o Acellular = at some point, they are not the form of a cell & cannot replicate ▪ Viruses - Smallest microbes - Require a host - Cause range of diseases, cancers ▪ Viroids - Infectious agents composed of RNA ▪ Satellites - Nucleic acid enclosed by protein shell - Coinfects host with a virus to complete life cycle ▪ Prions - Infectious proteins
• Types of microbial cells o Prokaryotic cells ▪ Lack true membrane-bound nucleus o Eukaryotic cells ▪ Membrane-enclosed nucleus ▪ Complexity

Koch’s Postulates Postulate Experimentation

1. The microorganism must be present in every case of the disease, but absent from healthy organisms Koch developed a staining technique to examine human tissue. M. tuberculosis could be identified in diseased tissue
2. The suspected microorganisms must be isolated & grown in a pure culture Koch grew M. tuberculosis in pure culture on coagulated blood serum
3. The same disease must result when the isolated microorganism is inoculated into a healthy host Koch injected cells from the pure culture of M. tuberculosis into guinea pigs. The guinea pigs subsequently died of tuberculosis.
4. The same microorganisms must be isolated again from the diseased host Koch isolated M. tuberculosis in pure culture on coagulated blood serum from the dead guinea pigs

• Limitations o Some organisms cannot be grown in pure culture o Using humans = unethical o Molecular & genetic evidence may replace & overcome these limits Development of Techniques for Studying Microbial Pathogens
• Koch’s work led to discovery/development of… o Agar o Petri dishes o Nutrient broth & nutrient agar o Methods for isolating microorganisms
• Charles Chamberland (1851-1908): development of porcelain bacterial filters o Extracts from diseased plants had infectious agents present which were smaller than bacteria & passed through filters ▪ Filtered water still caused non-disease plants to develop disease o Infectious agents later shown to be viruses
• Edward Jenner (1749-1823): vaccination against smallpox o Observed milk maids to be ‘resistant’ to smallpox o Inflicted a person with a minimal amount of the disease
• Pasteur & Roux : discovered that incubation of cultures for long intervals between transfers caused pathogens to lose ability to cause disease o “Attenuated” bacteria or viruses = grown in environment they aren’t typically grown in, causing the microbial to mutate in order to adjust o Body can still have an immune response without being affected by the disease
• Alexander Flemming : discovery of the first antibiotic (penicillin) o Left an uncovered petri dish of staphylococcal bacteria, which become contaminated with mold o Observed the bacteria in proximity to the mold colonies were dying Second Golden Age of Microbiology
• Discovery of… o Restriction endonucleases o First novel recombinant molecule o DNA sequencing methods o Bioinformatics & genomic sequencing & analysis

Major Fields of Microbiology

• Medical microbiology: diseases of humans & animals
• Public health microbiology: control & spread of communicable disease
• Immunology: how the immune system protects a host from pathogens
• Microbial ecology: relationship of organisms with their environment
• Agricultural microbiology: impact of microorganisms on food production
• Food microbiology: microbes used to make food & beverages as well as spoilage microbes
• Industrial microbiology: antibiotics, vaccines, steroids, etc.
• Microbial physiology: metabolic pathways of microorganisms
• Microbial genetics. Molecular biology, & bioinformatics: nature of genetic information & how it relates to development & function CHAPTER 2: VISUALIZING MICROORGANISMS Microscopy
• Microorganisms range in size (nm-200 micrometers)
• Lenses: create images by bending light o Refractive index: measure of how greatly a substance slows the velocity of light ▪ Direction & magnitude of bending is determined by the refractive indices of the 2 media forming the interface
• Light enters & bends, potentially slowing
• Light exits & bends, potentially accelerating o Focus light rays at a focal point ▪ Distance between center of lens & focal point ( F ) = focal length ( f ) ▪ Short focal length = more magnification
• More space between lens & focal point causes light to scatter & disrupt image
• Resolution: ability of a lens to separate or distinguish small objects that are close together o Wavelength of light = major factor ▪ Shorter wavelength = greater resolution
• Working distance: distance between the front surface of lens & surface of cover glass or specimen when it is in sharp focus
• Oil immersion objective: when air is replaced with immersion oil, light ways that different enter the objective due to reflection & refraction at the surface of the objective lens will—increasing resultion

• Confocal microscope o Creates a sharp, composite 3D image of a specimen by using laser beam aperture to eliminate stray light, and computer interface ▪ Laser used to excite specimen ▪ 3D image due to multiple composites taken at different angles ▪ Only light from the focal place is sued to make up the image o Numerous application—study of biofilm Staining of Specimens
• Purpose o Increase visibility of specimen o Accentuates specific morphological features o Preserves specimen
• Fixation: preserves internal & external structures, fixing them in position o 2 types ▪ Heat fixation
• Preserves overall morphology, not internal structure o Doesn’t preserve internal detail (too harsh, inactivates enzymes)
• Used with bacteria & archaea ▪ Chemical fixation
• Protects fine cellular substructure & morphology o Time-specific o Preservation of internal detail
• Used with larger, more delicate organisms
• Dyes: make internal & external structures more visible by increasing contrast with background o Basic dyes: have (+) charge, bind to (-) charged cell structures (nucleic acids, proteins, & surfaces of bacterial or archaeal cell structures) o Acidic dyes: have (-) charge, bind to (+) charged cell structures o Simple stains: single stain of any color used to determine size, shape, & arrangement of bacteria o Differential staining: divides microorganisms into groups based on their staining properties ▪ Used to detect presence or absence of structures
• Capsules, flagella ▪ Gram stain: divides bacteria into gram-positive & gram-negative based on differences in cell wall structure
• Thick peptidoglycan layer in gram-positive cannot be leached of stain by alcohol
• Steps o Crystal violet: cells stained purple o Iodine: cells remain purple o Alcohol: gram-positive cells = purple, gram-negative cells = colorless o Safranin: gram-positive cells = purple, gram negative cells = red/pink ▪ Acid-fast stain: high lipid content in cell walls is responsible for staining characteristics
• Makes organisms hard to stain—heat or another agent is also often necessary
• Useful for staining members of the genus Mycobacterium
• Staining without dye o Negative staining ▪ Heavy metals don’t penetrate specimen but render a dark background ▪ Used to study viruses & cellular microbes o Shadowing ▪ Coating specimen with a thin film of heavy metal on only one side ▪ Useful for virus particle morphology, flagella, & DNA o Freeze-etching ▪ Freeze specimen, then fracture along lines of greatest weakness

▪ Allows for 3D observation of shapes of intracellular structures Electron Microscopy

- How it works o Electrons replace light as the illuminating beam o Wavelength of electron beam is shorter than light, resulting in higher resolution (1000X greater) o Allows for study of microbial morphology in great detail - 2 types o Transmission electron microscopy ▪ Heated tungsten filament used to generate a beam of electrons ▪ Electrons cannot pass through glass—electromagnets focus beam ▪ Electrons that pass through specimen form image - Denser regions scatter more electrons, causing them to appear darker o Fewer electrons strike that area o Eelectron dense” ▪ Lenses & specimen are under a vacuum ▪ Electrons are deflected by collisions with air molecules o Scanning electron microscopy ▪ Electron beam scanned over specimen ▪ Secondary electrons: shower of electrons discharged from surface atoms - Trapped by detector, which emits light when struck by electrons - Light converted into electrical current - More secondary electrons = lighter image ▪ Produces an image from electrons released from an object’s surface - Image produced from electrons that scatter from specimen Light Microscope Transmission Electron Microscope Highest magnification 1,000-1,500 100,000+ Best resolution 0.2 micrometers 0.2 nanometers Radiation source Visible light Electron beam Lens type Glass Electromagnet Medium of travel Air High vacuum Specimen mount Glass side Metal grid Source of contrast Differential light absorption Scattering of electrons Focusing mechanism Adjust lens position Adjust current to magnetic lens CHAPTER 3: PROKARYOTIC STRUCTURES General Characteristics of Bacteria

• Prokaryotes: differences from eukaryotes o Lack membrane-bound nucleus, membrane-bound organelles, & internal membranous structures
• Shape o Cocci & rod = most common ▪ Diplococci: pairs ▪ Streptococci: chains ▪ Staphylococci: grape-like clusters ▪ Tetrads: 4 cocci in a square ▪ Sarcinae: cubic configuration of 8 cocci o Other ▪ Coccobacilli: very short rods ▪ Vibrios: comma-shaped rods ▪ Spirilla: rigid helices ▪ Spirochetes: flexible helices ▪ Mycelium: network of long, multinucleated filaments ▪ Pleomorphic: organisms that are variable in shape

Methods for Uptake of Nutrients

• Passive diffusion o No input of energy required o Molecules move from higher concentration to lower concentration ▪ Speed based on size of gradient o EX: H 2 O, O 2 , & CO 2
• Facilitated diffusion o No input of energy required o Molecules move from higher concentration to lower concentration ▪ Speed based on size of gradient o Uses membrane-bound carrier molecules (permeases) ▪ Induced conformational change ▪ Rate increases with concentration gradient o EX: glycerol, sugars, & amino acids
• Primary & secondary active transport o Energy-dependent ▪ Primary: energy derived from the breakdown of ATP ▪ Secondary: energy derived from proton motive force o Molecules move against gradient o Involves carrier proteins (permeases) ▪ Carrier saturation effect is observed at high solute concentrations o Types ▪ ABC transporters (ATP-binding cassette) - Primary active transporters use ATP - Consists of… o 2 hydrophobic membrane spanning domains o 2 cytoplasmic associated ATP-binding domains o Substrate binding domains

• Secondary active transport o Use ion gradient to cotransport substances ▪ Protons o Types ▪ Symporter : 2 substances move in the same direction ▪ Antiporter : 2 substances move in opposite directions
• Group translocation o Energy-dependent o Chemically modifies molecule as its brought into the cell o EX: sugar phosphotransferase system (PTS)
• Iron uptake o Ferric iron = insoluble, making uptake difficult o Siderophores secreted to aid in uptake ▪ Complex with ferric iron
• Transported into cell ▪ Often deliver iron to an active transport system Peptidoglycan (Component of Cell Wall)
• Present in most bacteria
• Structure o Rigid structure lying just outside plasma membrane o Mesh-like polymer ▪ Alternating sugars
• N-acetylglucosamine (NAG)
• N-acetylmuramic acid (NAM) ▪ Alternating D- & L-amino acids o Peptides crosslink peptidoglycan chains for strength ▪ Helical shape
• Two types (based on Gram stain) o Gram-positive: stain purple, thick peptidoglycan ▪ Composed primarily of peptidoglycan ▪ May contain teichoic acids
• Structure o Polymers of glycerol + ribitol joined by phosphate groups
• Function o Maintain cell envelope o Protect from environment o May bind to host cells ▪ May have layer of proteins on surface ▪ Periplasmic space between plasma membrane & cell wall
• Few proteins

o Also composed of sugars o Similar to capsules but more diffuse, unorganized, & easily removed o May facilitate motility

• Glycocalyx: aids in attachment to solid surfaces
• S-layers o Regular structured layers of protein + glycoprotein o Function ▪ Protect from ion & pH fluctuation, osmotic stress, enzymes, & predation ▪ Maintenance of shape & rigidity ▪ Adhesion to surfaces ▪ Protects from host defenses o In Gram-negative: adheres to outer membrane o In Gram-positive: associated with peptidoglycan CHAPTER 4: PROKARYOTIC STRUCTURE II Protoplast & Cytoplasm
• Protoplast: plasma membrane & everything within
• Cytoplasm: material bounded by plasmid membrane o Cytoskeleton ▪ Structure
• FtsZ (homolog of tubulin in eukaryotes) o Forms ring during septum formation in cell division o Helps to pinch off daughter cells
• MreB (homolog of actin in eukaryotes) o Determines shape in rod-shaped bacteria ▪ Absent in cocci ▪ If mutated, shape turns from rod to cocci o Maintains shape by positioning peptidoglycan synthesis machinery
• CreS (homolog of intermediate filaments in eukaryotes) o Rare, maintains curve shape o Unique to comma-shaped bacteria ▪ Function
• Participate in cell division
• Localize proteins
• Determine cell shape o Intracytoplasmic membranes ▪ Plasma membrane folds
• Increase respiration rate
• Observed in photosynthetic & high-respiratory activity bacteria o Inclusions (“microcompartments”) ▪ Stock-pile nutrients to be used when scarce
• Granules, crystals, or globules of material (organic or inorganic) ▪ Single-layered membranes
• Some made of protein, other lipids ▪ Types
• Storage inclusions: store nutrients, metabolic end products, energy, & building blocks o EX: glycogen, carbon, phosphate, & amino acids
• Microcompartments: compartments for specific functions o Not bound my membranes
• Gas vacuoles: provide buoyancy in aquatic, photosynthetic bacteria & archaea o Ribosomes ▪ Site of protein synthesis ▪ Bacterial ribosomal RNA = 70S = 30S + 50S
• 16S small subunit

• 23S & 5S in large subunit o Nucleoid ▪ Not membrane-bound ▪ Where chromosomes & associated proteins are located
• Usually 1 closed, circular, double-stranded DNA molecule = chromosome
• Can have up to 7, may be linear ▪ Supercoiling & nucleoid proteins aid in folding—histones o Plasmids ▪ Extrachromosomal DNA
• Exist & replicate independently of chromosome
• Episomes may integrate into chromosome(s) ▪ Small, closed, circular DNA ▪ Are virulence factors (enable bacteria to better cause disease) External Structures
• Extend beyond cell envelope
• Function o Protection o Attachment to surfaces o Horizontal gene transfer o Cell movement
• Types o Pili & fimbriae ▪ Structure
• Short, thin, hair-like protein appendages ▪ Function
• Mediate attachment to surfaces, motility, or DNA uptake
• Virulence factors ▪ Sex pili
• Exchange genetic information
• Longer, thick, less numerous
• Genes for formation of plasmids o Flagella ▪ Structure
• Threadlike, hollow appendages (20nm-20micrometers long)
• Ultrastructure composed of 3 parts o Filament: hollow, rigid cylinder, extends from cell surface to tip o Basal body: series of rings that drive flagellar motor ▪ Gram-negatives: 4 ▪ Gram-positives: 2 o Hook: short, curved segments that link filament to the basal body ▪ Function
• Motility, but can be used for attachment
• Virulence factors ▪ Types
• Monotrichous: single flagellum
• Lophotrichous: small bunches or tufts of flagella
• Amphitrichous: flagella at both poles
• Peritrichous: flagella dispersed randomly all over surface ▪ Synthesis
• New flagellin transported through the hollow filament using Type III-like secretion system
• Subunits self-assemble at tip with help of filament cap ▪ Motility
• Types

o Spore surrounded by exoporium: thin covering o Spore coat: thick layers of protein o Cortex: beneath coat, thick peptidoglycan ▪ Basis of vegetation o Core = nucleoid + ribosomes

• Sporulation o Endospore formation o Occurs over several hours o Initiated when growth ceases due to unfavorable conditions o Multistage process Formation of Vegetative Cell
• Stage 1: activation
• Stage 2: germination
• Stage 3: outgrowth

CHAPTER 5: EUKARYOTIC STRUCTURE

Eukaryotic Microorganisms

• 2 common microbial groups o Protists o Fungi
• Characteristics o Membrane-bound nuclei o Membrane-bound organelles with specific functions o Intracytoplasmic membrane complex = transport system o More structurally complex & larger than bacterial & archaeal cells Eukaryotic Organelles
• Cell envelopes o Consists of plasma membrane + external coverings ▪ Membrane lipids include sphingolipids, sterols, & phospholipids ▪ Microdomains participate in a variety of cellular processes
• Regions of membrane with greater concentration of lipids o Lack or have a chemically distinct cell wall ▪ Photosynthetic algae have cellulose, pectin ▪ Fungi have cellulose, chitin, or glucan
• Cytoplasm o Consists of cytosol + organelles o Cytoskeleton ▪ Interconnect network of filaments (homologous to bacterial proteins: FtsZ, MreB, & CreS)
• Microfilaments (actin) o 4-7 nm in diameter o Organized into networks & parallel arrays o Motility & shape changes
• Intermediate filaments o 10 nm in diameter o Structural role, form nuclear lamina (structural integrity of nucleus) o Link cells together to form tissues
• Microtubule

▪ Free ribosomes: non-secretory/nonmembrane proteins

• Mitochondria o Thought to have evolved from bacterial cells ingested by ancestor eukaryotic cells ▪ Similar to bacterial cells in that they reproduce by binary fission & size o Function ▪ “Powerhouse” ▪ Site of tricarboxylic acid cycle ▪ ATP generation via ETC & oxidative phosphorylation o Structure ▪ Outer membrane - Contain porin proteins ▪ Inner membrane - Highly folded = cristae - Location of ETC & oxidative phosphorylation ▪ Matrix - Contains ribosomes, mitochondrial DNA, enzymes of tricarboxylic acid cycle, & catabolism of fatty acids
• Chloroplasts o Function ▪ Photosynthetic reaction ▪ Pigment-containing (plants & algae) o Structure ▪ Stroma (matrix within inner membrane) - Contains DNA, ribosomes, lipid droplets, starch granules, etc. - Site of dark reactions of photosynthesis o Formation of carbohydrates from water + CO 2 ▪ Thylakoid (within stroma) - Site of light reactions of photosynthesis o Formation of ATP & NADPH
• Flagella o 100-200 micrometers in length o Move in undulating fashion o Basal body directed synthesis of new flagella/cilia
• Cilia o 5-20 micrometers in length o Beat with 2 phases, work like oars o Basal body directed synthesis of new flagella/cilia Degradation of Proteins
• Quality assurance mechanism o Unfolded or misfolded proteins secreted into cytosol ▪ Ubiquitin targets proteins for destruction ▪ Proteasomes destroy targeted proteins Endocytosis
• Function o Bring materials into cell o Solutes taken up & enclosed in vesicles pinched from plasma membrane o Material are then delivered to lysosomes for digestion (typically)
• Types

o Phagocytosis ▪ Use of cell surface protrusions to surround & engulf particles ▪ EX: destruction of bacteria o Clathrin-dependent ▪ Clathrin protein-coated pits used to internalize hormones, growth factors, iron, & cholesterol o Caveolin-dependent ▪ Signal transduction, transport of small molecules (folic acid) & macromolecules

• Clathrin-coated vesicles & some caveolin-coated vesicles deliver contents to endosomes o Early endosomes develop into late endosomes o Endosomes then fuse with lysosomes o Phagosomes fuse with lysosomes CHAPTER 6: MICROBIAL GROWTH Reproductive Strategies
• Binary fission (most bacterial cells) o Replication & segregation of genome occurs prior to division
• Budding?
• Multiple fission?
• Spore formation? Bacterial Cell Cycle
• 3 phases o Period of growth after cell is born (similar to G1) ▪ Increase in cytoplasmic volume ▪ Increase in number of ribosomes o Chromosome replication & partitioning (similar to S & M)