Notesale: Turn your study into money

Document Preview

Extracts from the notes are below, to see the PDF you'll receive please use the links above

---

Intro to Micro
Thursday, January 28, 2016
3:17 PM
 What is it- the study of organisms too small to be seen without magnification
 Microorganisms and corresponding fields of organisms study include:
 Bacteria = bacteriology
 Fungi = Mycology
 Protozoa = Protozoology (Parasitology)
 Represent Protista
 Algae = phycology
 Viruses = virology
 (Protista - single celled eukaryotic organisms do not confuse
o

o

o

o

with bacteria)
Importance of Microorganisms:
 Foundation for all life on earth
 Existed for most of earths history
 Plants, animals, modern microorganisms all evolved from bacteria
 Life depends on their activities
History of Modern Micro
 Antony van Leeuwenhoek
 Clothe merchant
 Made simple magnifying glass - observed animalcules
 Robert Hooke
 Observed samples of cork, coined the term "cell"
Ubiquity & Diversity of Microorganisms
 They can be found basically everywhere
 Many can be found in most given environments
 Early on this made it seem like they occurred through spontaneous generation
 Modern biology hinges on Cell theory (Schleiden, Shwann and Virchow)
 Unit of life is it has to be at least one cell
 Main contributors to disproving spontaneous generation
 Francesco Redi
 Louis Pasteur
 John Tyndall
Dispute of Spontaneous Generation
 Francesco Redi
 Demonstrated worms on rotting meat came from egg of flies landing on meat
 Meat in two jars on covered and one not
 Took another 200 years to convincingly disprove spontaneous generation of
microorganisms
 Due to dispute of different laboratories
 John Needham demonstrated boiled broths till had growths
 Father Spallanzi contradicted Needhams results
 Louis Pasteur
 Demonstrated air is filled with microorganism
 Filtered air through cotton plug
 Then improved upon it using swan neck flask















Germ Theory
o Microorganisms have a negative role
o Certain ones have certain roles
o Two major Scientists involved in asepsis (basically being clean or sterile:
 Ignaz Seemmelweiss - introduced hand washing in medicine after trying to figure out
why there was a much higher mortality rate with physicians when delivering babies
 Joseph Lister - introduced the use of antiseptic agents in medicine, sterilization of
instruments
Golden Age of Microbiology
o Major contributors to the discovery of Germ Theory
 Louis Pasteur
 Robert Koch (Koch's Postulates) : is it involved in every case, identify it, test it
o Many pathogenic bacteria identified
o Work on viruses (filterable agents) began
o Understanding that these organisms could cause disease lead to control effects of them
Immunology & Chemotherapy
o Edward Jenner
 Develops 1st vaccine against smallpox - not until 20th century did it become practical
o Eli Metchnikoff discovers phagocytic cells (cells to eat and protect the body) which begins
the study of immunology
o Paul Ehrlich begins the age of chemotherapy by discovering the 1st truly selective Salvarsan
(derivative of Arsenic)
o Flemmings discovery of penicillin followed & sulfa drugs by Domagk began the Golden Age
of Antibiotics
Microbiology: A Human perspective
o Could not survive without microorganisms
o Numerous benefits
o Microorganisms have also killed more people than have ever been killed in war
 Even often used in weapons
Host Microbe Interactions
o All surfaces of the human body populated by microorganisms
o Beneficial microbes
 Termed normal microbiota or normal flora
 Prevent diseases by competing with pathogens
 Development of immune system response
 Aid in digestion
 May cause disease (opportunists)
o Pathogens - damage body tissues -> disease symptoms
Microorganisms in the Environment
o Recycling nutrients
o Oxygen production through photosynthesis
o Nitrogen fixation
o Decomposers of material
 Cellulose degraded in the environment and the digestive tracts of ruminants
Applications of microbiology
o Food production
 Baking bread through yeast
 Egyptian bakers even used as early as 2100BC















Fermentation of grains to produce beer
Fermentation of milk
o Biodegradation
 Degrade PCB's, DDT, trichloroethylene and others
 Clean oil spills
 Bioremediation: using microorganisms to hasten decay of pollutants
 Synthesize commercially valuable products
 Cellulose, BIOFUELS, antibiotics, dietary supplements etc…
o Biotechnology
 Use of microbiological and biochemical techniques to solve practical problems
o Genetic Engineering
 Introduction to genes into another organism
 Disease-resistant plants
o Microorganisms as model organisms
 Wonderful model organisms
 Metabolism, genetics same as higher life-forms
Medical microbiology
o Most microorganisms are not harmful
o Some are pathogens
 Cause disease
 Influenza
Present and Future Challenges
o Despite impressive progress much work remains
 Very true for viral diseases and diseases associated with poverty
 Respiratory/diarrheal diseases cause most illness' and deaths in world
 Large rise in resistance to antibiotics in these microorganisms
o In US 750million infections
 200,000 deaths
o Costs billions
Domain = highest taxonomic level
o Three domains
 2 are prokaryotic: bacteria and Archaea
 One is Eukaryotic the Eukarya = 4 kingdoms
 Eukarya separates into multiple kingdoms
 Algae and protozoa are protists
 Then there are the fungi
Then there are the Acellular Infectious Agents - not alive by definition
o Viruses, Viroids, prions
Members of the Microbial World
o Enormous numbers
 Present in all environments on Earth
 Considerations of biodiversity typically overlook enormous contribution to microbes
 Less than 1% of all microbial species can be grown and studied in laboratory's
o Two cell Structures Prokaryotes and Eukaryotes
Taxonomy: organizing, classifying, and naming living things
o Classification - orderly arrangement or organisms into groups
o Nomenclature - assigning names

o

Identification - determining and recording traits of organisms for placement into taxonomic
schemes
o Identification, Classification, Nomenclature
 Bi-nomial naming system = genus and species
Classification & Identification of Bacteria
 Glimpse of History o Bacteria 1st classified by shape
o Carl Woese - Started Molceular Taxonomy
 Prokaryotes divided into two major groups based upon ribosomal RNA sequences
 Leads to current 3 domain system: Bacteria, Archaea, Eukarya
 Taxanomic Hierarchies
o Species - basic unit: group of morphologically similar organisms capable of producing fertile
offspring
 Problematic for prokaryotes
 Species is a group of closely related isolated or strains(members w/n species that vary
very slightly)
o Information groupings also used
 May be genetically unrelated
o Phylogeny - is evolutionary relatedness (uses three domain system)
 Principles of taxonomy
o Bergey's Manual of Systematic Bacteriology
 Describes all known species, has 5 volumes (each deals with different types of
bacteria),
 Use Phenotypic characteristics to identify Prokaryotes
o Culture characteristics, microscopic morphology = inspection, metabolic capabilities = for
identification, serology & fatty acid analysis = advanced techniques
o Culture characteristics can give clues
 Different colors at different temps with different smells
o Different (because separates organisms into 2 groups) Media aids in identification
 Certain microorganisms produce different things on certain agars
 Microscopic Morphology: important initial step
o Quickly determines size, shape, & staining characteristics
 Sometimes enough to diagnose eukaryotic infections
o Gram stain distinguishes + &  Possibly enough to start appropriate therapy
 Metabolic capabilities:
o Biochemical tests provide certainty of identification
 Catalase test
 Most rely on pH indicators
o Basic Strategy relies on Dichotomous key (basically decide which way to go at a fork in the
road during the experiment)
 Flowchart of tests with positive or negative tests
 Simultaneous inoculating speeds process
 Serology - use of specific antibodies
o Proteins, polysaccharides or pro's cells can serve as identifying markers
o Most uses include surface structure of cell wall, capsule, flagella, pili
o Use antibodies for detection
Using genotypic Characteristics to Identify Prokaryotes



Detecting specific nucleotide sequences
o Tests identify unique to species or group
 Nucleic acid probes locate nucleotide sequence characteristics of species or group
 Nucleic Acid amplification tests NAAT's used to increase number of copies of specific DNA
sequences
o Allows detection of small numbers of organisms
 Sequencing of Ribosomal Genes
o Sequences are stable
 Mainly because sequences would not function with too many mutations
 16S rRNA most useful because of moderate size (1500nuceotides)
 Sequence is compared with extensive database
identifies organisms that cannot be cultured

 Characterizing Strains
o Foodborne illness
o Diagnosing certain diseases
o Forensic investigations of bioterrorism, biocrimes
 Biochemical typing: group with characteristic pattern--biovar or biotype
 Serological Typing: group with characteristics antigens--serovar or serotype
 Molecular typing: patterns called restriction fragment length polymorphisms (RFLPs)
 Phage Typing: relies on difference in susceptibility
 Classification historically based on phenotypic traits
o Size, shape, staining, metabolic capabilities
 Phylogenetic tree--branches are twisted because the tree is not perfect
o Horizontal gene transfer complicates things (getting genetic info from other organisms)
Prokaryotic Cell Structure
 Two Domains: Bacteria Archaea
 Pro's smaller size gives high surface area to low volume
o Rapid uptake of nutrients & excretion of the waste = rapid growth
Morphology of Pro Cells: Shapes

o Two types most common:
 Coccus- spherical
 Rod- cylindrical
o Variety of other shapes:
 Vibrio, spirillium, spirochete
 Pleomorphic (many shapes)
 Great diversity often found in low nutrient environments
 Most pro's divide by binary fission then stick together after (diplo)
o Forms groupings
o Coccus- long chains
o Sarcina- cubical packets
 Cytoplasmic membrane defines boundary of a cell (fluid Mosaic Model)
o Phospholipid bilayer embedded with proteins
o Hydrophobic tails face in--hydrophilic heads face out
o Semipermeable membrane
 Only water and gases can pas through
o Simple diffusion--movement from high to low concentration
o Osmosis--movement of water across permeable membrane due to unequal concentrations
 Hypertonic- low outside flows to high inside (cell shrinks)














Isotonic- don’t take in or release (cell stays the same)
Hypotonic- low inside cell to high outside cell (cell swells up against cell wall)
Cytoplasmic Membrane and Energy Transformation
o Electron transport chain embedded in membrane
 Critical role in converting energy into ATP
o Use energy from electrons to move protons out of cell
Transportation of small molecules
o Most pass through proteins as selective gates
 Termed transport systems
o Facilitated diffusion-- a form of passive (passive because no ATP required) transport that
involves a carrier
o Active transport-- requires energy
 Movement against the gradient
 Two main mechanisms: proton motive force & ATP
o Group Translocation
 Chemically altered compound (changing a chemical to make the cell think it is not in
there
 Common technique is phosphorylation
o Bulk Transport- Endocytosis: take materials in using invaginations
 Pinocytosis-- bring fluid into cell by wrapping around it and dragging in
 Receptor mediated = same thing just specialized
 Exocytosis is reverse of endocytosis
 Plants, bacteria, and fungi cannot do endocytosis because of cell wall
Cell wall
o Strong rigid structure that prevents cell lysis
o Design of it distinguishes between two main groups of bacteria
 Gpositive (has peptidoglycan)
 Gnegative (lacks as much peptidoglycan)
 Second membrane called the outer membrane
o Peptidoglycan: sugar and protein parts
 N-acetylmuramic acid (NAM)
 N-acetylglucosamine (NAG)
 Print out powerpoint for this chapter
 Lipo teichoic acids go through the peptidoglycan go through cell wall and link into the
membrane to help anchor it down
o Penicillin -- does not effect gram negative cells because cannot reach peptidoglycan due o
outer membrane
o Shock caused by endotoxins can be made worse by antibiotics because once the bacteria
are killed they only release more endotoxins
o Lysozyme: in every single secretion that we emit--breaks bonds in glycan chain
Some bacteria lack cell walls
o Mycoplasma species have extremely variable shape
o Strengthen cell membrane by using sterols
o Must live within the body
Cell walls in Archaea
o Have variety of cell walls
o No peptidoglycan in cell wall










Many have S-layers that self assemble and are very hard to open
Tough walls because tough environments
Capsules and Slime Layers
o Gel like layer outside of cell wall that protects & allows attachment to other surfaces
 Capsule--thicker well defined material
 Slime-- diffuses and is irregular
 Most are composed of glycocalyx or polypeptides
 Once attached cells grow biofilms
 Community of these cells
Appendages
o Flagella
o 3 parts: filament, hook, basal body
 Involved in motility
 Numbers and arrangements are involved with characterization
 Peritrichous means they are all around the cell
 Polar only one flagella
 Amphitrichous one flagella one either end
 Lophotrichous a few flagella on one end
o Sense where they are going using the chemical gradient Chemotaxis
 Swims towards or away from specific chemicals
 Biasrandom walk
o Pili: shorter than flagella
 Fimbriae- allow attachment to other surfaces
 Sex pilus- used to join bacteria for DNA transfer (conjugation)
 Twitching motility and gliding motility involve special pili
Internal Components:
o Chromosome- forms gel like region: the nucleoid
 Single circular double stranded DNA
o Plasmids- circular supercoiled dsDNA
 Usually smaller; not essential for basic cell function
o Ribosomes: involved in protein synthesis (reason for the grainy look of cytoplasm)
 Facilitate joining of amino acids
 Pro's: 70S
 Euk's: 80S
o Cytoskeleton- internal protein framework
 Similar to Euk's actin (the thinest)
o Storage Granules- accumulations of polymers
o Gas Vesicles- controlled to provide buoyancy



---