Chapter 1: Introduction to the Microbial World Flashcards Preview

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Flashcards in Chapter 1: Introduction to the Microbial World Deck (70):

What is the definition of microbiology?

The study of organisms which can't be seen with the naked eye.
L> Study of micro-organisms (viruses, bacteria, fungi, algae, protozoa)


How are organisms scientifically named?

- Genus + species
L>first letter of genus is capitalized
L> species is lower case
L> ex: Escherichia coli -> E.coli (underlined)


What are two methods of studying microorganisms?

- microscopy
- cultures on plates or in broth


What are the types of microscopy ?

1. Light Microscopy
2. Transmission Electron Microscope (TEM)
3. Scanning Electron Microscope (SEM)
** 2 and 3 = Electron Microscopy
4. Fluorescent Microscopy


Give a description of characteristics of a light microscope!

- involves a bright field
-stained specimens( needed for looking at individual organisms)
- can use phase contrast for unstated specimens


Light microscopy:
-how do you calculate magnification?
L> maximum mag?

- objective x ocular
- magnification max= ~ x1500
Ex: ocular is x10...objective x10 = 100x mag


Light microscopy:
- resolution limit?

- limit of resolution for light microscope is about 0.2um
** ability to differentiate two things close together!


Electron Microscopy:
- Explain some characteristics of Transmission Electron Microscopes (TEM)

-can study internal structures within cells
- thin sections of whole cells
-negative staining with heavy metals (osmium, lead, uranium )
- high resolving power
-can see molecules

**electrons pass through the specimen (must be dead)


Electron Microscopy:
- Explain some characteristics of Scanning Electron Microscopy (SEM)

-can study external features
-intact cells and appendages
- specimen coated in heavy metal (gold)
-3D images
-magnification 15x to 100, 000x
-electrons bounce off the specimen
-can see shapes and they group
- magnification is not as high
- false colour is added


Give some characteristics of fluorescent microscopy!

-shine light at one wavelength- specimen emits light at another wavelength
- some materials fluorescence (chlorophyll)
-biomolecules labelled with fluorescent dyes
-real time and in living cells
-high levels of detail
-you just label the component of the cell you are interested in


Explain the importance of staining specimens with relation to light microscopes!

- basic dyes bind to cellular components which increase contrast for the bright field


What are differential stains?

- gram stains (divides bacteria into 2 fundamental groups with different cell walls)
-spore stain: very resistant to get dyes into
-fluorescent dyes
- negative staining for TEM
L> Negative staining is an established method, often used in diagnostic microscopy, for contrasting a thin specimen with an optically opaque fluid. In this technique, the background is stained, leaving the actual specimen untouched, and thus visible. This contrasts with 'positive staining', in which the actual specimen is stained.


What are the two different ways microbes can be cultured?

- surface of agar
- liquid culture


What can you study with surface agar?

- study characteristics
-can establish a pure culture (single colony)
- aseptic technique


What can you study with suspension agar?

- grow large quantities
- study biochemical and growth


Many thousands of bacteria form what on a plate?

- colony
L> each colony represents the descendants of a single organism (~1 million)
L> they are all genetically identical
L> colony appearance can be used in identification


How can you get a single colony on a plate?

- diluting via streaking
**mutations can occur that would make them not genetically identical


How old is the earth?

4.6 billion years old


Describe the earth in the first billion years (atmosphere wise)

- no oxygen
- mainly N2 and CO2


Approximately 3.9-3.8 bya on the planet what microbes came about?

- methanogens (methan producing) do not require oxygen


Approximately 3.6 bya on the planet what microbes came about?

- phototrophic (harvest energy from sunlight)


Approximately 2.6 bya on the planet what microbes came about?

- cyanobacteria produce oxygen
L> via waste product.....they rapidly changed
the atmosphere
**endosymbiot theory


What is the estimated total number of microbial cells on earth?



Where can microbes live?

- aquatic environments: rivers, lakes, oceans
- terrestrial environments: up to 10k below the surface
- inside living organisms: 500 to 1000 species of bacteria in the human gut which is similar to the skin. (10^10 in mouth...10^14 in gut)


Describe microbial communities!

- they usually live in mixed communities
-the populations interact
-waste products from one may be nutrients to another
- microbes interact with and change their physical environment (such as the mouth making teeth smooth)


Whats a big difference between microbial communities in nature vs lab?

- in labs they tend to be individuals


What are three important areas microorganisms are important for in research?

- biotechnology
- disease


Importance of microorganisms:
- biotechnology?

- bread, cheese, beer, wine, antibodies, vaccines, vitamins, enzymes, sewage disposal


Importance of microorganisms:

-major cause of human and animal disease


Importance of microorganisms:
- Ecology?

- carbon, oxygen, nitrogen, sulphur cycles. Basic level of all food chains.


History of Microbiology:
- spontaneous generation?

- Spontaneous generation from a nonliving substance such as meat and mud etc.
-ex: meat left exposed to approx a week, maggots will come out of it.
**these agents can also be infectious


Antoni van Leeuwenhoek's discovery (1632-1723)?

- discovered bacteria using a very simple microscope.
**first microscope


Robert hooke's (1635-1703) discovery?

- drew the fruiting bodies of old and looked at them through a microscope he developed.
(more advanced micro)


What is spontaneous generation?

- organisms arise spontaneously from non living material
eg: meat left to go bad will be found to contain bacteria and maggots


Louis Pasteur (1822-1859) discovery??

-- he proposed that microorganisms from the air and surfaces were the source
- nutrient solution was sterilized by boiling
- Swan neck allowed air into the flask but prevented microorganisms from entering it. Open to air but microorganisms couldn't get in..


Microorganisms in disease:
-John Snow (1813-1858)?

- epidemiology of cholera in London
- removed the handle of the broad street pump and halted to the cholera epidemic
**people drinking this water were getting cholera


Microorganisms in disease:
-Joseph Lister (1827-1912)?

- pioneered the use of antiseptics in surgery
-used phenol compounds on dressings and as a spray
**reduces risk of infection


Microorganisms in disease:
-Robert Koch (1834-1910)?

- worked on Bacillus anthracis
- showed that bacteria were always present in the blood of an animal with anthrax
**isolated organisms and cause anthrax in another animal


Microorganisms in disease:
- Koch's Postulates?

- the disease causing organism must always be present in the animal with the disease and not present in healthy animals
-the organism must cause disease when inoculated into a healthy animal
- the organism must be reisolated and cultured


- Edward Jenner(1748-1823)?

- introduced cowpox vaccination for smallpox.
*introduced them to a little boy.


-Martinus Beijernck (1851-1931)?

- discovered viruses by selectively filtering
-showed the presence of an infectious agent smaller than bacteria
- also showed they were associated with the cells
**filtered out bacteria showing that filtrate was still able to cause diseases i.e. something else is there -> virus
**work on tobacco mosaic virus


-Wendall Stanley (1904-1971)?

- showed viruses were particulate
- crystallized them, redissolve them and cause diseases still aka not living


- Fred Sanger (1918-)?

- First complete genome sequence
- bacteriophage X174( 5,636bp)


Molecular Microbiology:
- Werner Arber (1929-)?

- discovered restriction endonucleases
-gene cloning possible now


Molecular Microbiology:
- When was the first bacterial genome sequenced?

- 1995
- Haemophilus influenzae (1.83Mb)


Molecular Microbiology:
- Describe advances in microbial genome sequencing in 2015

- at least 3029 whole bacterial genomes
-834 whole fungal genomes
-4466 viral genomes


Model Organisms:
-What is a model organism?

- one that has been extensively studied as an example of many others from which general principles may be established
L> biochemistry, physiology and genetics


Model Organisms:
- characteristics?

- small size and short generation time (mouse, drosophila, arabidopsis)
*genotype sequence available for most model organism
**r-selected species


Model Organisms: Bacteria
-Which ones were discussed in Julia's lectures?

1. E. coli
2. Bacillus subtilis
3. Mycoplasma genitalium
4. Saccharomyces cervisiae


Model Organisms: Bacteria
- E. coli characteristics?

- gram negative
- easy to grow
- easy to manipulate
-model organism for microbial physiology, biochemistry and molecular biology
- found in human colon
- closely related pathogenic and harmless strains


Model Organisms: Bacteria
-characteristics of Bacillus subtilis?

- gram positive
- spore forming (differentiation = forming spore...1 of the simplest models to study this)
- found in soil, water sources and in association wit plants


Model Organisms: Bacteria
- characteristics of Mycoplasma genitalium?

- a minimal organism (smalletest genome... 10% of the size of E. coli)
- host associated but can be cultured in the laboratory
- defective in several biosynthetic pathways
- genome 580 kbp (compared to E. coli 4600 kbp)
-470 ORFs (genes)
-Synthetic life: the genome has been synthesized and put into a genome free mycoplasm


Model Organisms: Fungi
- characteristics of Saccharomyces cerevisiae ?

- bakers yeast
- budding yeast
- quick and easy to grow
- cell cycle studies (similar to humans, homologous regulatory proteins)
- eukaryotic
- similar to mammalian making it a model for cell cycle


Microorganisms as cells undergo which processes?

- metabolism, reproduction ** all
- differentiation, communication and movement = only some organisms


- Compartmentalization?

- cell membrane separates the cytoplasm from the enviornment


- characteristics of it?

- uptake of nutrients
- chemical transformation of nutrients
- energy storage and utilization
- elimination of waste


- metabolic versatility??

- some pseudomonas bacteria can use antibiotics as a source of carbon and nitrogen
-microbes can live in very extreme environments
- all natural and most synthetic compounds can be broken down by one or more organisms (usually into harmless products)
**extremophiles --> leads to this diversity



- production of new substances or structures
- common in multicellular organisms
- fungi produce fruiting bodies
L> mushrooms/toadstools
L> spores both asexual and sexual
Ex: Rhizopus sexualis and Penicillium sp


Differentiation: Bacteria
- how can it occur?

- asymmetric division producing two different daughter cells
**binary fission is more common
- Endospores (resistant to heat and desiccation )
- Motile and sessile forms
Ex: Bacillus anthracis and Caulobacter


Reproduction (growth):
-Prokaryotes (bacteria and Archea)

- single circular chromosome
- nucleoid - aggregation of DNA but not membrane bound
- binary fission is the norm


Reproduction (growth):
- Eukaryotes (fungi and protists)

- membrane bound nucleus
- several linear chromosomes
- budding (yeast) -> can tell the age of them by budding scars
L> budding is common in single cells


- Quorum sensing
L> three characteristics?

1. bacteria assess the population density
2. Regulate gene expression
3. Autoinducer molecular


- Quorum sensing
1. bacteria assess the population density

bacteria assess the population density (ensuring sufficient numbers before initiating a response)


- Quorum sensing
2. Regulate gene expression

-Regulate gene expression via population density ( toxin production in pathogenic bacteria, luminescence in Vibro fisherii and biofil formation in Pseudomonas)


- Quorum sensing
3. Autoinducer molecular

-Autoinducer molecule
L> eg: Acyl homoserine lactone in Pseudomonas
L> small and highly diffusible


Explain quorum sensing!

- low bacterial numbers, low concentration of autoinducer, expression of specific genesis down regulated.
- dense bacterial population, high concentration of auto inducer, auto inducer expression up regulated, expression of specific genes is down regulated
***aka need a high concentration for an effect to occur
**genes are activated by inducers


-movement towards __ and away from __.

- nutrients
- waste products


- What are the three ways movement can occur?

1. Flagella
L> Bacterial: many bacteria, flagella propel bacteria
L> eukaryotic: dinoflagellates
2. Cytoplasmic Streaming
ex: Amoeba ..push membrane forward
3. Cilia:
ex: paramecium ... hairlike structures that help it move


Explain characteristics of bacterial flagella?

- composed of flagellin arranged in a helix
- flagella filament is helical
- rotary motor in the cell membrane
- flagella rotate like a propeller to cause movement


Explain characteristics of Eukaryotic flagella (cilia)!

- composed of microtubules (tubular and dynein)
- sliding of microtubule filaments gives a whip like movement
- do not rotate
- cilia are essentially short flagella