microbio test 1

hippocrates

“father of western medicine”

thucydides

• father of scientific history

• early concept of immunity

marcus terentius varro

proposed that things we cannot see could cause disease

al-Razi (rhazes)

• experimental methods to test aspects of medicine

• meat rotting & hospital location

• efforts to identify disease cause, not just focus on symptoms

ibn sina (avicenna)

• canon of medicine

• described contagion, infection, and transmission

• illness isolation & quarantine

leeuwenhoek

used magnifying lens to observe “animalcules” in rain drop

• father of microbiology

Louis Pasteur 

• Fermentation and spoilage caused by microbes  

• Pasteurization  

• Vaccines (e.g. rabies)  

Robert Koch  

• Established method for connecting pathogen with specific disease 

• Koch’s postulates  

• Anthrax, cholera, tuberculosis  

Phylogenetic analysis  

Molecular techniques were implemented by Woese & Fox 

Strains  

• Closely related genetic variants within a species  

• Sublevels: kingdom, phylum, class, order, family, genus, species, strain 

Naming organisms 

• Binomial nomenclature – two-word system that names organisms based on genus and species  

• Names generally have Latin or Greek roots 

• Written out in italics 

• Genus is capitalized; species is lower case 

• Genus can be abbreviated after initial use 

Cellular Microbes 

• Prokaryotes  

- Bacteria  

- Archaea  

• Eukaryotes  

- Protists  

- Fungi 

- Helminths  

Acellular microbes  

• Viruses 

• Prions  

Archaea  

• Different evolutionary history, genetics, metabolism, physiology from bacteria 

• Pseudopeptidoglycan  

• Extreme environments 

Protists

algae, protozoa, water molds & slime molds 

Algae

plant-like; photosynthetic and important in ecosystems and consumer products  

Protozoa

animal-like: very diverse and backbone of many food webs 

Water molds

fungal-like; (oomycetes) often parasites or decomposers

Slime molds

fungal-like; “intelligent” and have both single-and multicellular life stages  

Fungi 

• Multicellular and unicellular (yeasts)  

• Chitin cell walls 

• MOLDS: good & bad  

Helminths  

• Multicellular parasitic worms 

• Microscopic eggs and larvae  

Viruses and Prions

• Acellular  

• Require a host to reproduce 

• Prion: proteinaceous disease-causing agent 

chapter 2 starts here : )

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Properties of light 

• Wavelength = length between peaks  

• Amplitude = height of peaks  

• Frequency = rate of peaks in time 

Lower wavelengths

lower frequency

Light interactions 

• Reflection = wave bounces off material 

• Absorbance = wave is captured 

• Transmission = wave travels through  

• Interference = interacts w/ another wave 

• Diffraction = bent or scattered by object opening 

• Refraction = change direction and/or speed 

Refraction  

• Refractive index – degree of change in transmission speed  

• Higher refractive index causes more bending light 

refractive index = speed of light in vacuum / speed of light through material

Convex lens refraction occurs on a curved boundary to meet a focal point (microscope)  

Concave lens refracts light away from a focal point (flash lights)  

Electromagnetic radiation spectrum 

• Higher frequency waves have higher energy (photons move faster) 

• Certain materials can refract non-visible into visible (e.g fluorescence)  

Magnification

ability of a lens to enlarge the image of an object (microscopes refract light to magnify images) 

Contrast

visible differences between parts of a specimen through brightness or intensity; enhanced by staining  

Resolution

ability to tell that two separate points/objects are separate  

wavelengths

SHORTER wavelengths = HIGHER resolution

LONGER wavelengths = LOWER resolution

Antonie van Leeuwenhoek

utilized 1st simple microscope 

Galileo Galilei

used a compound microscope 

Robert Hooke

• first to describe “cells” using compound microscope and observing cork cells 

Darkfield microscopy  

• Brightfield with modified condenser with an opaque disk (light stop) 

• Light that is viewed through objective lens is reflected/refracted from specimen 

• Good for viewing live specimen and/or ones that cannot be stained 

Phase contrast microscope  

• Increases contrast w/o stain 

• Good for viewing live specimen and organelles  

• Features are highlighted based on refractive index 

Differential interference contrast microscope  

• Similar to phase contrast 

• Two different wavelengths are passed thru specimen and combined for differential effects 

Fluorescent microscope  

• Fluorochromes are used to absorb & refract into visible light 

• Direct & indirect (immunofluorescent) 

Confocal microscope  

• Scans multiple z-planes 

• Thick specimen  (e.g. biofilms) 

• Modified fluorescence to avoid “bleaching” 

Two-photon microscope

• Good for viewing thicker materials (brain slices, embryos, organs, etc) 

• Modified confocal scope near with near infrared light  

• Minimizes light scattering through tissue 

Electron microscopy  

• Recall: resolution is limited by wavelength  

• Electron microscopes use electrons and have short wavelengths (no use of light) 

• Two types  

1. Transmission electron microscope (TEM) 

2. Scanning electron microscope (SEM) 

Transmission electron microscope  

• Forms image based on varying opacity of specimen\ 

• Specimen are cut very thin 

• View internal structures  

Scanning electron microscope  

• Electrons are bounced off specimen w/ coating 

• Surfaces are easily observed

TEM 

• Samples analyzed must have very thin sections (ultramicrotome)  

• Specimen embedded in plastic resin and dehydrated 

• Stained with electron dense heavy metals  

SEM 

• More dehydrated – critical point drying with liquid CO2 

• Sputter-coated with metal 

Staining specimen  

• Wet mount – good for viewing live specimens 

• Fixed mount (smear) -- good for staining 

Basic stain

positively charged ions 

Basic fuchsin, crystal violet, malachite green, safranin, methylene blue 

Acidic stain

negatively charged ions 

Eosin, rose Bengal, acid fuchsin 

Positive stain

Dye/stain is absorbed into cells 

Negative stain

Dye/stain absorbed into background

simple stains

• emphasizes structure

• single stain

differential stains

• differentiates organisms based on stain interactions

• 2+ stains

gram stain

• distinguishes diff cell wall components

• important clinical diagnostic tool

gram stain (STEPS)

1. primary stain (crystal violet)

2. mordant (iodine)

3. decolorizer (alcohol)

4. counter stain (safranin)

pink = negative 

purple/violet =  positive 

acid fast stain

• diagnostic tool for detection of mycolic and Mycobacterium spp

• Ziehl-Neelson method (w/ heat)

• Kinyoun method (w/o heat)

acid fast stain (STEPS)

1. heat fix smear

2. primary stain (carbolfuschin)

3. decolorizer

4. counter stain (methylene blue)

endospore stain

• identification of endospore formers

• Schaeffer Fulton method

endospore stain (STEPS)

1. heat fix smear

2. primary stain (malachite green)

3. decolorzier (water)

4. counter stain (safranin)

capsule stain

• diagnostic tool for detection of protective coating

• dyes do not penetrate capsule

capsule stain (STEPS)

1. no heat smear

2. primary stain (india ink)

flagella stain

• identification of flagella appendages

• bacteria, archaea, eukaryotes

flagella stain (STEPS)

1. no heat smear

2. primary stain (specialized)

3. decolorizer (water)

4. counter stain (carbol fuschin)

chapter 3 starts here : )

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cell theory

• robert hooke - cork tissue “cells” (1665)

• matthias schleiden - plant tissue (1838)

• theodor schwann - compared plant and animal cells (1839)

• robert remak - cells come from other cells (1852) cell division

• rudolf virchow - published “cellular pathology” (1855) “all cells arise from cells”

endosymbiotic theory

• lynn margulis (1967) - mitochondria and chloroplasts of prokaryotic origin

• ^^ 1981 - symbiosis and cell evolution

• DNA, ribosomes, binary fission

**** mitochondria and chloroplasts were orginally prokaryotic cells thar established a symbiotic relationship within a eukaryotic host

germ theory of disease

Diseases may result from microbial infection 

• Girolamo Fracastoro (1546) 

• ”spores” can be transferred between individuals 

• Ignaz Semmelweis (1847) 

• “Contaminated” physicians transferred causative agent to patients 

• Promoted handwashing as solution 

• John Snow (1848) 

• cholera outbreaks in London traced to sewage in drinking water 

louis pasteur (1856)

• organisms could spoil food and therefore people

joseph lister (1857)

• handwashing + carbolic acid in surgery for disinfection

robert koch (1884)

• koch’s postulates - a specific microbe can cause a specific disease

the prokaryotic cell

• nucleoid

• inclusions

• plasmids

• pili

• fimbriae

• endospore

nucleiod (prokaryotic cell)

• Central region of cell w/ DNA & DNA associated proteins 

• Chromosomes(s) are circular and haploid  

• Plasmids – circular, non-essential DNA 

Prokaryotic ribosomes  

• Sites of protein synthesis 

• Prokaryotic – 70S size (50S + 30S) 

inclusions (prokaryotic cell)

• Structures used for storage of excess nutrients, movement, or specialized metabolism 

• Storing nutrients in a polymerized form aids in reducing osmotic pressure 

endospores (prokaryotic cell)

• Structure formed in dormant state to protect genome 

• Most resilient state of bacteria and primary goal/target for sterilization processes  

• Vegetative cells are present in normal favorable conditions 

Cell (plasma) membrane  (prokaryotic cell)

• Present in all organism 

• Has selective permeability to move molecules in and out 

• Bilayer of phospholipids linked with esters and embedded with proteins and carbs 

membrane transport mechanisms

• passive transport - diffusion of molecules

• facilitated transport - carrier proteins that ferry larger molecules across w/o ATP

• active transport - membrane proteins that move molecules with ATP

• group translocation - molecule chemically modified as it enters a cell against unfavorable concentration gradient

cell wall (prokaryotic cell)

• Found outside the cell membrane  

• Function is to protect cell from adverse conditions 

• Different for bacteria, archaea, and eukaryotes 

• Peptidoglycan (bacteria) is a major component and provides shape 

• Components include alternating chains of N-acetylglucosamine & N-acetylmuramic acid with different linkages 

Cell Wall: Archaea  

• Pseudopeptidoglycan 

• Similar to some bacterial species 

• A few archaea do not have cell walls 

Glycocalyces  

• Glycocalyx = sugar coat outside cell wall that allows cells to adhrere to surfaces, protect against desiccation and/or antibiotics and disinfectants  

• Capsules = organized; polysaccharides or proteins 

• Slime layer = loosely attached and made of polysaccharides, glycoproteins, or glycolipids  

S-layer 

- composed of structural proteins and found outside cell wall 

- provides rigidness and helps against osmotic pressure changes  

Filamentous Appendages 

• Fimbriae = short bristly proteins that aid in attachment 

• Pili = longer appendages aid in attachment OR transfer of DNA  

Prokaryotic Flagella  

• Structures used to move in aqueous environments towards an enviromental signal  

• Phototaxis = light 

• Chemotaxis = chemicals  

• Magnetotaxis = magnetic fiels 

• Aerotaxis = oxygen 

• Basic structures includes; basal body, hook, & filament  

• Different bacteria have different arrangements  

• Movement and direction occurs by changing rotation of the flagella  

Nucleus (eukaryotic cell)

• DNA material is surrounded by a membrane  

• ^^ chromosomes are linear 

Nucleolus (eukaryotic cell)

• dense region in nucleus where ribosomal RNA (rRNA) is synthesized

ribosomes (eukaryotic cell)

• 80s (40s small subunit + 60s large subunit) 

• ^^ chloroplasts & mitochondria have smaller (70s) ribosomes (recall prokaryotes)  

Endomembrane system  (eukaryotic cell)

• Function = create and move components around within the cell  

• Included organelles: 

- Endoplasmic reticulum (smooth & rough) 

-Golgi apparatus 

-Lysosomes 

-Vesicles  

Endoplasmic reticulum  (eukaryotic cell)

• Group of tubules & flat sacs 

• Function = synthesis of various molecules 

• RER – ribosomes are present & synthesizes proteins 

• SER – NO ribosomes and synthesizes lipids, metabolizes 

Golgi apparatus  (eukaryotic cell)

• Membranous disks stacked together 

• Function = modifies lipids & proteins that arrive from ER 

• Vesicles carry modified molecules to other parts of the cell  

Lysosomes  (eukaryotic cell)

• Membrane bound organelles that contain digestive enzymes 

• Function = to break down food, damaged organelles or cellular debris  

Peroxisomes (NOT part of endomembrane system) 

• Membrane bound organelles that produce hydrogen peroxide 

• Function = contribute to lipid synthesis as well as degradation of molecules  

• Some can be socialized and modified  

Cytoskeleton

• Filaments inside the cell that provide structure and network for transport 

Microfilaments (cytoskeleton)

• Involved in cell motility, cytoplasmic streaming, cell division, muscle movement 

• Amoeba locomotion 

• Pseudopodia – temporary extensions of membrane that fill with microfilaments  

Intermediate filaments  (cytoskeleton)

• ^^^ diverse group of monomers that act as cables within the cell  

• Mid-size component of cytoskeleton  

• Anchor nucleus and other organelles, and form nuclear lamina