microbiology exam 1

chapter 1, chapter 2, chapter 3, chapter 4, chapter 5

microbe

microbe

a living organism that requires a microscope to be seen

types of microbes

eukaryotes (fungi, protists), bacteria, archaea, viruses

most microbes

acquire food + energy, reproduce, evolve rapidly, sometimes form communities + populations

microbial capabilities are defined by their

genome sequence

polymerase chain reaction

using heat stable DNA polymerase to identify pathogens

virus

noncellular particle with a genome that invades a cell to produce more virus

genome

total genetic information in an organism’s DNA, used to produce a metagenome (the first sequenced bacterial genome was H. influenzae via Sanger sequencing)

uses of microbes in society

yeast + bacteria are used for food + beverage production, and metal mining

bubonic plague

14th century, Yersinia pestitis, spread by rat + human fleas

tuberculosis

19th century, mycobacterium tuberculosis

florence nightingale

created a polar area chart to show how soldier’s most common cause of death was microbial infections

medical statistics can also reveal

health disparities

Robert hooke

used the first compound microscope to observe mold, published micrographia (illustrated objects under the microscope), coined the term cell

Antonio van leeuwenhoek

single lens magnifiers with sample holder + focus adjustment, show w/ hot coffee that heat can kill microbes

spontaneous generation

living organisms can arise spontaneously with no parents

franceso redi

showed hat maggots in decaying meat were the offspring of flies

Lazzaro spallanzani

sealed flask of meat broth sterilized via boiling failed to grow microbes, discovered cell fission (splitting of preexisting cells)

louis pasteur

discovered fermentative metabolism (sugars into alcohol via yeast, presence of oxygen results in acetic acid, otherwise alcohol)

pasteurs swan necked flasks

microbes were trapped in the neck of the flask and when introduced to sterilized broth, microbes grew, proving oxygen is not needed (flasks don’t allow admission of oxygen)

life first arose from

nonliving organisms

germ theory of disease

many diseases are caused by a specific pathogen/microbe

Robert koch

studied anthrax, established chain of infection, made pure culture of tuberculosis via gelling agent (agar) and Petri dish

koch’s postulates

1. microbes are found in all cases of disease

2. microbe isolated from diseased host and grown in cultures

3. microbe causes disease in healthy susceptible host + host shows same disease

4. same strain of microbe is obtained from newly diseased host

caveats to koch’s postulates

1. microbes with low infectious doses (HIV+ AIDS)

2. absence of animal hosts who share same disease + symptoms (H. pylori)

3. complicated disease cycles (vectorborne disease)

4. viruses

immunization

stimulation of an immune response by deliberate innoculation w/ attenuated pathogen

killed pathogen vaccine

pathogens that have been grown in culture and killed to destroy disease causing capacity

live attenuated vaccine

weakened form of pathogenn

toxoid vaccine

using toxoid as antigen to induce immune response

Ignaz Semmelweis

noticed doctor-pathogen transmission during childbirth, chlorine handwashing protocol

Joseph lister

developed antiseptics (chemical that kills microbes) leading to aseptic (microbe - free) environments)

antibiotics

kill microbes but not the host

Alexander Fleming

discovered penicillin (penicillin mold shown to kill staphylococcus) - antibiotics are generated by microbes

wendell stanley

purified tobacco mosaic virus

tobacco mosaic virus

viral proteins form a helical tube surrounding RNA, resolved using x ray crystallography

RNA viruses

influenza, HIV, ebola, RSV

river’s postulates

a specific virus must be regularly associated w/ a disease and the virus must be shown to be the cause of the disease (not an accidental finding)

environmental microbiology

how microbes interact w/ the environment + each other

microbial ecology

study of relationships + interactions within microbial communities

winogradsky column

used to take samples of microbial communities in sediment

microbes cycle

all N2 and most O2, and can survive deep in earth’s crust and in the stratosphere

enrichment culture

using selective growth media to allow particular microbes to grow

nitrogen fixation

form of geochemical cycling where microbes reduce NH3 to a form of nitrogen that plants can consume

extremophiles

grow only in extreme conditions (heat, salinity, acidity)

endosymbionts

microbes living symbiotically inside a larger organism (cannot be isolated via pure culture)

microbiota

organisms/microbes on/inside a living organism, contributed to by endosymbiotic microbes

microbiome

organisms/microbes associated with a living organism, contributed to by endosymbiotic microbes

geochemical cycling

cycling of nitrogen, phosphorus and other minerals via bacteria + archaea

challenges in microbe classification

microscope resolution too low, species hard to define (distinct species <= 95% similarity in DNA sequences)

monera (microbes are not plant or animal, but)

eukaryotic protists (protozoa + algae) + prokaryotic bacteria

serial endosymbiosis theory (Lynn margulis)

mitochondria + chloroplasts evolved via intracellular endosymbiosis from prokaryotic cells engulfed by pre-eukaryotes

archaea

prokaryotes who differ equally from bacteria + eukaryotes

polyphyletic ancestry

ancestry from multiple descendants

electron microscope allowed for

more magnification, revealing of internal cell structure

centrifuge

separates whole cells from fluid

ultracentrifuge

separate lysed cell components

rosalind franklin

discovered DNA double helix via x ray crystallography, as well as RNA helical form

Watson and crick

discovered the 4 DNA bases + base pairs

DNA sequencing

reading of a sequence of DNA base pairs

Har Gobind Khorana

codons, first synthetic oligonucleotide, role of mRNA

DNA advances in bacteria

DNA recombination, PCR, gene regulation, CRISPR-Cas9 bacterial defense system

transformation

internalization of free DNA from environment into bacterial cells

detection

the ability to determine the presence of an object

magnification

increasing an object’s apparent dimensions to resolve smaller separations between objects

filamentous rods

rods (bacilli)

spirochetes

light microscopy (commonly bright field microscopy)

object perceived as dark object blocking the passage of light

maximize observation of detail via

wavelength + resolution (wavelength must be less Than or equal to size of the object)

light + contrast (objects and its surroundings should not radiation equally)

lens quality

objective lens

situated directly above the object/specimen

angle of aperture

widening the nose of the cone of light, maximize resolution by adding light

empty magnification

size of an image increases with no increase in resolution

wavefronts undergo

interference

as lens strength increases and light cone width increases the lens must

come closer to the object

immersion oil

use between object and lens at 100x, prevents refracted light

compound microscope

system of multiple lenses designed to correct or compensate for lens aberrations

diaphragm

allow for control of light on specimen (high powered lenses require more light)

condensors

lenses that collect beams of light from the light source

total magnification

ocular lens (10x) x objective lens magnification

wet mount

placing microbes in a drop of water, must use slide cover

phase contrast microscope

cell outlines appear darker, dependent in the principles of interference

fixation

adherence to slide (usually kills) increasing detection + resolution

staining

uses molecules that absorb the light resulting in a distinctive color (usually kills) increasing detection + resolution

gram stain

gram positive - dark purple

gram negative - pink

simple stain

adds dark color specifically to cells

differential stain

colors one kind of cell but not another

gram stain

1. fix slides to cell with methanol

2. add crystal violet stain

3. add iodine and wait 1 minute

4. wash with ethanol

5. add safranin counterstain

acid fast stain

identifies mycobacterium

giemsa stain

used for blood cells and associated parasites

fluorescent microscopy

specimen absorbs light of a defined wavelength and emits lower energy light

can reveal specific cell parts at work (cell fission, protein division, etc)

fluorophore

fluorescent dye or protein

autofluorescence

natural emission of light by cell structures

induced fluorescence

usually done with a laser

fluorophores for labeling

chemical affinity, labeled antibodies (conjugated - immunofluorescence) , DNA hybridization (label chromosome positions)

gene fusion reporter

engineer cells to express a bacterial protein combined with GFP and other variants

bacterial cell membrane composed of

phospholipid bilayer, transport proteins, and other molecules

bacterial cell membrane

hydrophobic, prevents cytoplasmic proteins from leaking out, maintains ion and nutrient gradients

cell membrane proteins

half the mass of membrane, nutrient transport _ structure (anchor cell envelope, attach membrane to cytoskeleton, base of protruding structures), often function as a complex

cell membrane fatty acids

hydrophilic outer head interacts with water, hydrophobic inner tails, uniform thickness and stability required for structural integrity + function

membrane reinforcing agents

hopnanoids/hopanes, cholesterol

biosynthesis of lipids as a target for antibiotics

triclosan inhibits reductase (needed for lipid synthesis)