Microbiology Flashcards
How are relationships identified
Evolutionary evidence (fossil records)
Similarity of observable characteristics
genetic similarities and evolutionary relatedness
What are the three domains of life
Bacteria, archaea and eukaryotes
What is the order that domains are broken down in
Life, Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species
What are the rules of binomial nomenclature
Genus name is always capitalized, can be abbreviated
Species name is always lower case can not be abbreviated
Always italicised (typescript) or underlined (written text)
What makes up domain eukarya
Microscopic algae, microscopic fungi, protozoa, helminths
What makes up domain archaea
archaeabacteria
What makes domain bacteria
Eubacteria (true bacteria)
what are the problems with algal blooms
turns the tide red. Can be harmless but could cause problems from toxins or accumulated biomass
Describe fungi
Can be multicellular or single cellular yeasts. Some cause mold or disease
What fungi causes black mold on food
Aspergillus niger
Explain how protozoa-1 work
Cyst is injected, converts into trophozoite which can be excreted (Giardia lamblia)
Explain what helminths are and how they work
Protazoa-2 types of worm and nematodes. They are often parasitic and ingestion of eggs causes diseases
What are archaeabacteria
Prokaryotes that are distinguished from domain bacteria. They may be considered ancient organisms and many live in extreme environments
define thermophiles
organisms which grow at extremely high temperatures
Define psychorophiles
organisms that thrive at extremely low temperatures
Define halophiles
organisms which live in conditions of extreme salinities
Describe mathanogens
organisms which live in anaerobic conditions and produce methane
How do archaea distinguish from bacteria
Their ribosomes structure
types and linkages of lipids
Variations in RNA polymerase
Difference in cell wall
Lack of peptidoglycan
What is the difference between gram positive and gram negative bacteria
Gram positive bacteria have a thick layer of peptidoglycan on the outside of the plasma membrane. Gram negative has a thinner layer and an outer membrane
What are some ways bacteria can gain energy
photoautotrophs gain energy from light
methanotrophs gain energy from methane
chemolithotrophs gain energy from inorganic molecules
chemoorganotrophs gain energy from organic chemicals
What did Anthony van Leeuwenhoek discover
in 1676 he saw animalcules (what we would call microscopic organisms) in a water sample. He made the monocular microscope
What is spontaneous generation and how was it disproven
The belief that living organisms could develop from non-living organisms (maggots from rotting meat, fleas from hair etc.)
Francesco Redi disproved it using a 3 jar experiment
What is Lois Pasteur known for
Pasteurization (aseptic techniques), showing microbes caused fermentation, developed anthrax and rabies vaccine
what is a simple microscope
A microscope with only one lens
What is a compound microscope
microscopes that contain an eyepiece and one or more additional lens. Light is directed onto specimen using condenser lens. Can be monocular or binocular
Why is blue light used in microscopy
has shorter wavelength and can improve resolution
describe the objective lens
Mounted on a rotating head it can provide different magnification
Describe the eyepiece lens
A magnifying lens. Usually x10
How do you calculate total magnification
Objective lens + eyepiece lens
how does immersion oil improve resolution
this is due to oil having the same refractive indices to glass
Describe light field microscopy
Specimens are stained with dyes to improve contrast. This allows visualization of specimens showing size and morphology
Describe dark field microscopy
Allows image contrast but without using a stain which can introduce artifacts. The specimen causes light to scatter and unscattered light is excluded. Lights specimen from sides and backlights it.
Describe phase-contrast microscopy
A beam of light is spit in two passed through the specimen and then reunited to form an image. The specimen which has different refraction index causes phase variation
Describe fluorescence microscopy
An excitation light is shone on a sample which the itself emits a coloured light. Fluorecent dye molecules that attach to parts of specimen. The microscope uses a laser beam to scan on/through the specimen.
Gives a high resolution visualization and quantification of 3D structures
Describe electron microscopy
Electron microscopy can be used to magnify images over 100000 times. Similar to light microscopy but at much higher magnification
Describe scanning microscopy
Scanning electron microscopy (SEM) is beams of electrons that scan surface of the specimen making £D images from the scattered electrons and other particles
Describe transmission microscopy
TEM is beams of electrons emitted into vacuum and focused on specimen. Electrons pass through or are scattered. Scattering visualised
What are the two types of specimen preparation
Wet and hanging drop mounts and fixed mounts
describe Wet and hanging drop mounts
Microscopy specimens are mounted
Wet and hanging drop mounts allows live cells to be examined for motility shape and arrangement
Describe fixed mounts
A specimen fixed onto a slide by gently heating it. Specimen is stained to allow improved visualization
Why do you stain specimens
Most bacterial cells are colourless and detail is hard to see. Provides more contrast. enhances visibility of specimen details
Describe chromophores
chromophores have a ring structure with an unbonded electron which can be positively or negatively charged. They are responsible for giving each dye its characteristic colour
What is cationic dyes
basic dyes with positive charges on chromophore. Bind to nucleic acids many proteins and cell membrane. The most widely used dye
What are examples of cationic dyes
Methylene blue, basic fuchsin, crystal violet
Describe anionic dyes
Acidic dyes with negatively charged chromophore. They bind to positively charged structures
Give some examples of Anionic dyes
Eosin, acid fuchsin
What are differential stains
the use of two or more dyes. These are usually a primary stain and a counter stain.
Describe gram stains
Gram stains distinguish the two classes of bacteria based on cell wall structure. They can be positive or negative. The key feature is peptidoglycan that provides rigidity.
How do you do a gram stain
Cells are fixed and and first treated with crystal violet, the primary stain, before being washed with iodine. Cells are treated with acetone then counterstained with basic fuchsin or safranin
Describe gram positive cells
Cells have a thick layer of peptidoglycan that traps crystal violet. They stay blue/purple
Describe gram negative cells
cells that have a thin layer of peptidoglycan and more easily release the CV-mordant complex. They end up with a pink colour
Describe the features of a typical prokaryotic cell
2-10um in length, intracellular have a plasma membrane, a nucleoid, pili, flagellum and glycocalyx
Describe the bacterial nucleiod
its a single circular chromosome free in cytoplasm. There is no surrounding membrane but genome includes plasmids and extra-chromosomal elements
It complexes with DNA binding proteins
What comprises the bacterial cell envelope
The inner plasma membrane, the cell wall and exterior layers including capsule, polysaccharide or slime
Describe bacterial cytoplasmic membrane
semi-porous, permeable to specific molecules, has a phospholipid bilayer, hydrophilic to outside hydrophobic to inside
How is movement across membranes done in bacterial cells
simple diffusion, facilitated diffusion and active diffusion.
Describe the bacterial cell wall
part of the cell envelope, made of peptidoglycan, determines cell shape, prevents osmotic lysis and is target for some antibiotics as its recognized by host system
What are the differences between gram positive and gram negative peptidoglycan
Gram negative has a more open structure and fewer bonds than gram positive
describe the gram negative outer membrane
unusual and highly complex. It is an asymmetric phospholipid bilayer featuring several surface exposed molecules that play a role in virulence
what is unusual about Mycoplasma
It is pleomorphic meaning it has no cell wall. It is parasitic and requires a host to survive
What is lysozyme
an enzyme produced by eukaryotic cells and hydrolyses peptidoglycan to protect against bacterial infection
What are the three outcomes when bacterial cell wall is punctured/removed
Hypertonic, isotonic, hypotonic
define protoplasts
gram positive cells that have lost their cell walln
define spherolasts
gram negative cells that have lost their cell wall
what is the glycocalyx
comprised of glycoproteins and proteoglycans that are secreted onto the cell surface
what are flagella
whip like organelles specialised to allow motility. Common in all 3 types of life
what is an aflagellate bacteria
bacteria lacking flagella (this is typical in cyanobacteria
Define monotrichous
one flagellum protrudes from one end
Define Lophotrichous
several flagella protrude from one end
define amphitrichous
at least one flagellum at each end
Define peritrichous
flagella protrude from all over cell surface
How does the flagellum move the cell
They rotate in one direction (counterclockwise) and the bacterium moves forward.
Rotation in the opposite direction cause the bacterium to tumble and randomly change direction. Switching back to move forward
describe pili
thin protein tubes extending from the cytoplasmic membrane. Not involved in movement. They allow cells to adhere to receptors.
What are endospores
gram positive cells with a differentiated life cycle. They can form endospores a highly resistant structures that allow these bacterial species to withstand hostile condition by undergoing dormancy
How do endospores form
When nutrients are limited they germinate inside vegetative cells
Describe Staphylococcus aureus
Gram positive
Facultative anaerobes
Form in clisters
infects digestive tract, lung, urinary tract and skin.
Invasive
Describe Streptococcus pyogenes
Gram positive
Fermentative
Forms in long chains
Infects respiratory tract, skin
Invasive
Describe the 2 types of firmicutes
Non sporulating gram positive bacteria.
Endospores forming gram positive bacteria
they have low G+C (35-55%)
Describe the 3 types of actinobacteria
Rod shaped representatives
Acid fast group
Filamentous actinobacteria
They have high G+C (>65%)
Describe the Clostridium genera
Rod shaped
Obligate anaerobes
Spore formers
Describe the Bacillus genera
Rod shaped
Facultative anaerobes
Spore formers
Common in soil
Compare obligate anaerobes to facultative anaerobes
Obligate anaerobes are organisms that can grow and survive only in the absence of oxygen
Facultative anaerobes can grow with or without oxygen
How have Bacilli been used in biotechnology
They secrete a wide range of enzymes into their environment some of which have useful properties including serine protease, cellulase and alpha amylase
What is the agricultural application of Bacillus
they produce a “crystal protein” toxin when it sporulates that can be used as an insect pathogen
What is the medical application of Bacillus
some produce peptide antibiotics synthesized by a complex enzyme
Describe enterobacteriaceae
A large homogenous phylogenetic group of gamma proteobacteria
Facultatively anaerobic, gram negative and non sporulating rods
non motile
Oxidase negative and ferment sugars
Describe the Enterobacteriaceae family
Gram negative microorganisms including Escherichia, Salmonella, Shigella, Yersinia and Proteus
Define the term coliform
Bacteria with biochemical and morphological traits in common.
Gram negative, facultative anaerobes, non-spore forming rods, and they ferment lactose to acid and gas.
Describe E. coli
Gram negative, motile, facultatively anaerobic.
They are catalase positive, oxidase negative ad can ferment a range of carbohydrates to acid and gas
How are archaeal membranes different from bacteria and eukaryotes
Archaea lipids are unique in 4 ways
side chains are not fatty acids (isoprenes)
Ether linked lipids rather than ester linked
Different chiral form of glycerol
Some posses lipid monolayers
How is genetic transmission done in bacteria
Binary fission is asexual reproduction
Following replication genetic material bacterial cell divides forming two new individual bacteria
Describe vertical genetic transmission in eukaryotes (yeast)
budding off of daughter cells in yeast and binary fission of certain protozoa
What is recombination (bacteria)
bacterial genome recombining with DNA from phages and other bacteria
What are Amoebozoa
Diverse groups of terrestrial and aquatic protists. They move using pseudopodia and feed by phagocytosis. Include the Amoeba genus
What are slime molds
Originally thought to be fungi as found in habitats of fungi. Found in soil and decaying plant matter and feeds on E.coli
What does ‘fruiting bodies’ mean
macroscopic reproductive structures produced by some fungi (e.g. mushrooms)
Describe fungi
chemoheterotrophic
do not perform photosynthesis
Have cell walls that contain chitin
what is hyphae
network formed by multicellular fungi
What are conidia
hyphae that extend above the surface can produce asexual spores. They are often pigmented and resisatnt to trying
What are mycelia
Compact tufts formed by hyphae
How do fungi reproduce by asexual means
Most reproduce by asexual means
Growth and spread of hyphal filaments
Asexual production of spores
Simple cell division
How do fungi reproduce by sexual means
Sexual spores can originate from fusion of two haploid cell to form diploid cells
Describe fungal phylogeny
share a more common ancestor with animals than any other eukaryotic organisms. Estimated to have diverged 1.5 billion years ago
Describe Chytridiomycetes
the earliest diverging line of fungi. Commonly found in soil and freshwater. Some are colonial and some are unicellular
Describe Zygomycetes
Known for food spoilage
Enzymes for industry
Commonly found in soil and decaying plant material
All form zygospores
Describe Microsporidia
Unicellular, obligate parasites of animals and protists. Often infect immune compromised individuals.
Describe Glomeromycetes
Obligate symbionts
All known species form endomycorrhizae
Forms arbuscular mycorrhiza
Reproduce asexually only
Define endomycorrhizae
The fungus colonizes the interior of host plant root cells (arbuscular mycorrhizas)
What is arbuscular mycorrhizas
a form of endomycorrhiza that helps capture nutrients for plants
Describe Ascomycetes
Highly diverse
Found in aquatic and terrestrial environments. Decompose dead plant materials
Includes bakers yeast and penicillium
Describe Candida
ubiquitous fungi found throughout the world as normal body flora
Describe mushrooms and other basidiomycetes
Over 30000 described species
Many are mushrooms/toadstools as well as yeast and pathogens
they undergo both vegetative and sexual reproduction
Describe algae
Protists with chloroplasts
Most found in freshwater and marine environments
Most photoautotrophs
Reproduce a/sexually
How do algae reproduce
Asexual - Fragmentation, spores, binary fission
Sexual - gametes fuse to produce diploid zygotes
Describe green algae
Have chlorophylls a and b as well as carotenoids
Store carbs as starch
Wide variety of forms
cell walls of cellulose
closely related to plants
Describe Volvox
individual cells that form spherical colonies
Only a few cells are reproductive
Describe diatoms
Single celled or colonial
Cell wall consists of silica
have bilateral symmetry
major component of phytoplankton
Describe dinoflagellates
Mostly marine some freshwater
Important primary producers
phototrophic, heterotrophic and mixotrophic
Some bioluminescent
Unicellular
Lists, horns and spines used to identify species
What are lists
membranous thecal extensions of armored dinoflagellates
What are horns
contain cytoplasm and are covered in thecal plates and can be hollow or partially solid
Describe spines
solid projections that taper to a point
talk about toxic dinoflagellates
75% of worlds toxic marine microalgae are dinoflagellates. Toxins can cause seafood poisoning
what are zooxanthellae species
A group of dinoflagellates that form symbiosis with for example corals and jellyfish
what are the key characteristics of protozoa
unicellular
eukaryotic
non phototrophic
heterotrophic
many parasites
diverse life cycles
How to protozoa move
cilia, flagella, pseudopodia (can be non motile)
What is the distribution of protozoa like
free living in marine and freshwater environments, decaying organic matter in soil, moisture is a necessity. Some are parasites
what is a trophozoite
any stage in a protozoans life cycle which can injest food
What are cysts
non motile form which is protected by a distinct membrane or cyst well
what is a definitive host
where parasite reaches sexual maturity
what is an intermediate host
required by parasite to complete its life cycle. Usually undergoes morphological and physiological change in it
What is a vector
host that plays an active role in transmission can be a definitive or an intermediate host
Describe Sporozoa
All members are endoparasites. Apical complex. They have complex life cycles
Describe Ciliophora
Body covered in cilia arranged in rows or spiral
Appearance varies greatly
Most are fee living
define catabolism
breakdown of complex organic molecule into simpler compounds and releases energy
define anabolism
the building of complex organic molecules from simpler ones, requires energy
define autotrophic organism
organism that can make organic molecules from inorganic nutrients
define heterotrophic organisms
an organism that cannot make organic molecules from inorganic nutrients. Depends on organic molecules for energy generation and precursors for cell material
define phototrophs
photosynthetic - gets energy from sun
define chemotrophs
energy from oxidation of chemicals
what are redox reactions
= energy from oxidation - reduction reactions
Redox reaction occur in pairs
Electron donor (substance oxidized)
Electron acceptor (substance reduced)
explain catabolism
the breakdown of foodstuffs into small molecules. Has many pathways. Dependent on organism and environment
What are the 2 main energy generation strategies
Respiration and fermentation
Describe respiration
aerobic or anaerobic catabolic where electron donor is oxidized
Described fermentation
anaerobic catabolism where organic compound is both electron donor and acceptor
describe cyanobacteria
Photoautotrophs that use atoms from water to reduce dioxide to form carbohydrates. First organism to photosynthesize
what are lichens
an association between fungus and cyanobacterium/algae
what is the biogeochemical cycle
flow of essential elements of living matter between abiotic and biotic components of Earth
How does carbon exists in the non-living environment
Carbon dioxide, carbonated rocks, deposits of coal petroleum and natural gas, dead organic matter
What is the carbon cycle
how carbon moves between the atmosphere, soils, living creatures, the ocean, and human sources
what is bioremediation
the use of microbes to restore stability or clean e.g. oil spills, chemical spills, water and sewage treatment)
describe co-metabolism
contaminants not used as a food source by transformed to less hazardous chemicals
mineralisation/oxidation
contaminants used as a food source and destroyed
describe biodegradation of hydrocarbons
respiration of the hydrocarbons to carbon dioxide - can be aerobic or anaerobic
describe anaerobic biodegradation
breakdown of organic compounds in the absence of oxygen. uses alternative electron acceptors.
describe biostmulation
adding nutrients to the contaminated soil or groundwater in order to enhance the biodegradation of hydrocarbon contaminants
describe bioaugmentation
microbial cultures are added to the contaminated site in order to have appropriate metabolic capability to degrade hydrocarbon contaminants
what are bioplastics
biodegradable plastics - potential answer to plastic waste
how is waste water treated
Stage 1 - screens trap rubbish
stage 2 - stones and grit are removed
Stage 3 - water rest in tanks where any solids sink to bottom becoming sludge which is pulled out to be treated
Stage 4 - good bacteria are grown in the tanks to eat potentially harmless chemicals
Stage 5 - water allowed to rest again. Water is mixed and left over bits sink to bottom
Name some examples of biofuels
ethanol - from microbial fermentation of glucose
natural gas CH4 from anaerobic metabolism
conversion of waste product to ethanol/methanol
oil from soybeans
how is drinking water treated
Stage 1 - surface water is stored in reservoirs to meet demand
Stage 2 - water is passed through mesh screens to remove debris
Stage 3 - impurities in water are removed
Stage 4 - water run through filtration
Stage 5 - disinfection is vital to ensure diseases are eliminated.
Stage 6 - pH level is controlled
describe water purification
removal of disease causing organisms from waste water
Chlorination
UV light radiation
Ozonation
How do we detect pathogens in water supplies
we use indicator organisms coliforms and E. coli as they are indicators of fecal contamination
how are microbes associated with crops
soil microbiomes
nitrogen
fertilisers
biological nitrogen fixation
what is the rhizosphere
zone around plant roots where there is an increase in organic carbon called rhizodeposition
what promotes rhizobacteria
pathogen suppression, fixation of nitrogen, solubilization of mineral
what is nitrogen fixation
energy intensive process.
atmospheric - spontaneous (lighting)
industrial - Haber-Bosch process
biological - nitrogen fixing bacteria
What are ectomycorrhizae structures
fungal cells that form an extensive sheath around the outside of the root with only a little penetration into root tissue
what is the rumen
a special digestive organ possessed by certain herbivorous mammals.
describe fermentation in the rumen
rumen microbes hydrolyze cellulose to fee glucose that is fermented producing fatty acids that pass through into bloodstream and utilized for energy.
describe general features of viruses
they reproduce at high rate only in living host cells
their genome can mutate
they have no cytoplasm or organelles
they can grow or divide independently
usually have DNA or RNA but not both
describe size and shape of viruses
smallest are about 20nm largest 200-300nm
can be helical, icosahedral, or polyhedral
how are viruses classified
their geometry
whether they have an envelope
what organism they infect
their genome
how they transmit
what they cause
describe the core of virus structure
nucleic acid genome (RNA or DNA)
describe the protein caspid of virus structure
often made up of many copies of small proteins. provides protection and directs attachment to host cell
describe the helical virus structure
simplest way to arrange many copies of identical proteins.
Basic design RNA genome acting as a structure that basic binding proteins condense onto
describe icosahedral virus structure
rounded structure in which 20ntriangular faces form an icosahedron
how is the viral envelope formed
derived from host cell by budding
matrix proteins glue the capsid to the membrane
glycoproteins are anchored in the membrane which are essential for recognition/attachment
describe lytic growth
virus grows in its preferred site
After a few days host responds
immune response gathers momentum and the virus is removed from the system
or virus wins and the hist dies
describe lytic growth with latency
some viruses can remain dormant in nerve cells
a lytic episode such as the cold sore on the mouth is followed by immune response
virus remains latent and reappears in future
describe slow growth viral replication
slow diseases are typically characterized by slow development over many years
They often cause progressive neural damage and a fatal outcome and include immunodeficiency virus (HIV)
name modes of viral replication in humans
lytic growth, lytic growth with latency, slow growth, cancer
what does the infectious cycle typically include
attachment, penetration, uncoating, transcription/translation, replication, assembly, release
describe antibiotics
Natural anti-microbial substances produced by fungi and bacteria to compete with other micro-organisms for space and nutrients in soil - they kill them or stop them growing
Why are antibiotics important to humans
They can be used as drugs (e.g. penicillin)
Before antibiotics simple infected cuts or infections could go systemic and kill
describe genetic variation in bacteria
mutation - due to rapid division mutations can spread quickly
recombination - genome can recombine with DNA
Can lead to new strains with increased virulence or resistance
how are we going to combat antimicrobial resistance
Improve knowledge and understanding of AMR
Conserve ad steward the effectiveness of existing treatments
stimulate the development of new antibiotics, diagnostics and novel therapies
