Microbiology Flashcards
What did Robert Hooke do
wrote first book devoted to microscopic observations
What did Louis Pasteur do
disproved spontaneous generation by showing heat can be used to sterilise
What did Robert Koch
Microorganisms are often the cause of the disease. Developed Koch’s postulates by studying mice and anthrax and a disease caused by Bacillus anthacis.
Growing microorganisms
only some can be cultivated in a lab. Need to grow in a nutrient solution (culture medium). Requires careful preparation (right recipe, keep sterile). Can be solidified with agar or kept liquid
Why are tubes containing solid agar set on a slope
increases surface area, used for pure growth of a microorganism
Types of light microscopy
bright-field (staining can improve contrast, but kills specimen), phase contrast, dark field (improved contrast without killing cells). fluorescence (visualise cells that fluoresece e.g., chlorophyll)
Light microscope resolution
0.2 micrometres
Atomic force microscopy
measure forces between a probe and the atoms on the surface of the specimen, measures deviations from flat surface
Confocal laser scanning microscopy
couples a laser source to a fluorescent microscope, focuses through the specimen in layers into a 3D image, cells typically stained with fluorescent dyes to make them more distinct
Differential interface contrast microscopy
form of light microscopy, used polarised light (light in a single plane), cellular structures appear more 3D
Electron microsocopy
Uses electrons instead of visible light, electromagnets function as lenses, whole system operates in a vacuum
Transmission electron microscopy
high magnification, 0.2 nm resolution (high), can see structures at a molecular level, have to make thin section of a specimen - electrons don’t penetrate into tissues well
Scanning electron microscope
shows external surfaces of cells, intact specimen coated in a thin film of heavy metal like gold, electrons scatter from metal coating and are collected and processed to form image
Why study microbes
All cells have much in common so discovers made in microbial cells can be applied to multicellular organism
, Don’t take up much space , Grow rapidly, Easily manipulated , Useful and interesting
Archeae features
Only two phyla – the Euryarchaeota and the Crenarchaeota. Classification is difficult as the majority have not been isolated in the laboratory. Usually look similar to bacteria, but often have genes and metabolic pathways more similar to eukaryotes
Protozoa features
Unicellular eukaryotes , Live in soil, wet sand, fresh and salt waters, Great diversity in shape, mobility and metabolism
Algae features
Eukaryotes ,Contain chloroplasts , Have cell walls, Both terrestrial and aquatic
What size do prokaryotic cells range from
0.2 micrometres to > 700 micrometres in diameter
What cells do eukaryotic cells range from
10 micrometres to > 200 micrometres in diameter
Why is a higher SA:V an advantage to small cells
faster nutrient exchange so they can grow faster and support a large population
Why is faster evolution an advantage to smaller cells
higher mutation rate (higher rate of cell division) which is a raw material for evolution allowing rapid adaptation to changing environments
What is the disadvantage to small cells
can only just fit in all the essential cellular components
What are endosporesz
highly differentiated cells, produced by certain species of bacteria, highly resistant to heat/harsh chemicals/ radiation, survival structures (like a nuclear bunker)
What is sporulation
an essential nutrient is exhausted so vegetative cells stop growing, endospore develops within vegetative cell is released, can remain dormant for years, germinates into a vegetative cells when conditions are good
Endospore structure
strongly refractive and impermeable to most dyes, usually seen as unstained regions within cells
Fimbriae and pilli composition
filamentous structures composed of protein extending from surface of a cell
What are fimbriae
enable cells to stick to surfaces and each other
What are instances where fimbriae exisist
salmonella species, neisseria gonorrhoeae, whooping cough
Pili features
longer than fimbriae but only 1 or 2 present. Best seen under electron microscope when coated with virus particles
What are the functions of pili
conjugation (genetic exchange between cells), adhesion of pathogens to specific host tissue and subsequent invasion, can be involved in motility
What is microbial locomotion
cells can move under their own power, enabling them to reach different parts of their own environment
What are taxis - microbial locomotion
movement towards something that will aid growth or away from toxins
Taxi examples
chemotaxis - response to chemicals. Phototaxis - response to light
Flagellum in aiding cell movement
Rotate to push or pull through a liquid, found in both gram negative and gram positive bacteria. Only seen with light microscopy after being stained
What is polar flagellation
flagella are attached to one or both ends
What is a tuft of flagella
A group of flagella attached to one end of the cell
What is peritrichous flagella
Flagella inserted at many location
Flagella structure
helical, wavelength (distance between curves) is a characteristic for diff species, a molecular motor in the cell membrane drives rotation
Structure of flagellum molecular motor
Central rod, passes through a series of rings, mot proteins (act as stators). Rod and rings rotate while the mot proteins stay still
Where is the energy for rotation come from
proton movement across membrane through Mot complex, protons flow through channel, exert electrostatic forces on helically arranged charges on rings, attraction and repulsion between charges cause rotation. Like ATP synthase mechanism
How does the flagella change when there is an attractant present
there are longer runs and fewer tumbles
Gliding of cells
slower than swimming, cells must be in contact with a slid surface, colonies of gliding bacteria have distinct properties
Gliding mechanism - polysacchardie slime
connects cell surface with solid surface, as slime adheres to surface, the cell is pulled along
Gliding mechanism - twitching motility
repeated extension and retraction of type IV pili
What do myxobacteria form
multicellular structures - fruiting bodies
Features of fruiting bodies
often strikingly coloured and morphologically elaborate
What is the myxobacteria glide
Vegetative cells excrete slime to move across surface, leaves behind a slime trail
What is a myxobacteria swarm
slime trail is picked up by other bacteria, radiating pattern of established slime trails
Myxobacteria life cycle
- Myxospores are resistant resting cells released from sporangioles upon favourable conditions
- Myxospores germinate and form gram negative vegetative cells which divide to reproduce
- Vegetative myxobacteria are motile by gliding, forming visible slime trails
Myxobacteria life cycle 2
- Under favorable conditions, the vegetative cells swarm to central locations, forming an aggregation
- Aggregations of cells heap up into a mound, an early fruiting body
- Mounds of myxobacteria differentiate into a mature fruiting body, which produces myxospores packed within sporangles
What are the sources of carbon
eating something containing carbon or fixing your own
What is an autotroph
uses CO2 as their carbon source, primary producers, synthesise new organic matter
What is a heterotroph
uses organic compounds as their carbon source, either feed directly or on other cells or live off products other organisms excrete
What is a symbiotic relationship
cooperative relationship with the host
Parasitic relationship
antagonistic relationship with the host
Saprotrophic relationship
the host is dead
How do microbes get the energy they need to grow
chemical energy (chemotrophy) - organic (chemoorganotrophs) and inorganic (chemolithotrophs) and light energy (phototrophs)
Phototrophs - oxygenic photosynthesis
algae.green plants/cyanobacteria. CO2 into sugars. Light converts ADP into ATP. The reducing power is water to create oxygen
Phototrophs - anoxygenic photosythesis
purple and green bacteria. H2S is the reducing power creating SO4 2-. Light still used to convert ADP into ATP.
Chemoorganotrophs
oxidation of organic compounds releases energy stored as ATP can be aerobic or anaerobic
Chemoliphotrophs
oxidation of inorganic ions rleases ATP. Only in prokaryotes. e.g., sulphur and iron bacteria
What is nitrogen fixing
converts atmospheric nitrogen gas into a form that can be used by cells
Nitrogen fixation equation
N2 + 8H+ + 8e- –> 2NH3 + H2
What are the 2 types of nitrogen fixing bacteria
free living (no host) and symbiotic
Nitrogenase
catalyses nitrigen fixing. Made from dinitrogenase (contains iron and molybdenum, accepts electrons) and dinitrogenase reductase (contains iron and splits ATP)
What is nitrification
oxidation of inorganic nitrogen compounds, preformed in nitrifying bacteria (found in soil/water)
Nitrosomonas catalyse equation
2NH4+ + 3O2 –> 2NO2- + 4H+ + 2H2O
Nitrobacter catalyses equation
2NO2- + O2 –> 2NO3-
What is the importance of nitrogen fixation/ nitrification
part of plants productivity for sewage and waste treatments, removing toxic amines and ammonia
What is growth in multicellular organisms compared to single cell
the whole organism gets bigger in multicellular, single cellular is increase in number of cells in population
What is generation time
time taken for the cell to divide
What is generation time
time taken for the cell to divide
What are the steps of binary fission
- cell replicates its DNA
- The cytoplasmic membrane elongates separating DNA molecules
- Cross wall forms (septum) membrane invaginates
4.Cross wall form completely
5.aughter cells form
How does generation time vary
Variable between and within species depending on nutritional and environmental factors e.g., temperature and the competition in a habitat
What is a logarithmic scale
increases to the power of 10
Generation time formula
time/number of generations in time (gradient)
Final cell number formula
N2^n
N = initial cell number
n = number of generations during the period of exponential growth
number of generations during the period of growth formula
(log(N)-log(N0))/ 0.301
N = final cell number
N0 = initial cell number
What does exponential growth do
work in bases of 2 e.g., 2^6
When does the lag phase occur
time between when culture is inncoulated into fresh media and significant growth
What causes the length of the lag phase to vary
history of the inoculum, nature of the medium and growth conditions
When does a longer lag phase occur
when cells are depleted of essential constituents, time is required for their biosynthesis e.g., poor medium used so they need to synthesise essential metabolites
What is the exponential phase
cells population doubles at regular intervals, the healthiest stsae
What causes the exponential phase to vary
availability of environmental conditions (temperature, nutrients etc) and genetic characteristics of the organism
What is the stationary phase
essential nutrient in culture medium runs out so waste products build up to toxic levels. Cell growth = cell death
What is the death pahse
exponential decline of viable cells, rate of cell death > cell division. Viable cells remain in culture for long periods of time
How to measure growth
microscopic counts, viable counts and spectrophometry
How do you carry out a microscopic count
Sample is dried and stained to increase contrast onto slides. Cells are counted in large squares and scaled up. Use a counting chamber of flow cytometer
Limitations of microscopic counts
Without special staining techniques, dead and live cells cannot be distinguished. Imprecise. Small cells difficult to see. Motile cells must be demobalised
What is a viable cell
a cell that is able to divide and produce offspring
What is the assumption made for viable counts
each viable cells will divide to form one colony
How do you carry out a viable count
Pipette a sample on to agar and spread evenly using a sterile glass spreader. Count colonies
Why is culture medium a source of error for viable counts
incubation conditions and incubation time have a big effect
Why is culture medium a source of error for viable counts
incubation conditions and incubation time have a big effect
may How is a mixed culture medium a limiting factor to viable counts
Not all cells grow at the same rate (different generation times), colony sizes may vary (miss small ones)
Other limitations of viable counts
inaccurate pipetting, non-uniform sample (cell clumps), insufficient mixing, heat intolerance
What is spectrophotometry
cells scatter light, turbidity can be used to estimate cell mass in a sample. More light scattering = more cell mass = more cells
What is microbial ecology
a given species lives in certain places but not others - environments differ in their abilities to support diverse microbial populations
What is an ecosystem
a dynamic complex of plants, animals and microbial communities and their non-living surroundings, which interact as a functional unit
Microbes in an ecosystem
great metabolic diversity, primary catalysts of nutrient cycles, very important members of the ecosystem
Why do microorganisms have microoenvironments
are very small so only directly experience a tiny local environment. Metabolic activities from microorganisms alter the conditions
Why is diffusion important to microorganisms
Diffusion determines the availability of resources. Microorganisms near outer edges consume oxygen before it can diffuse into the centre so anaerobic organisms thrive in the centre and aerobic on the outer layers
How is oxygen concentration measured
using micro electrodes in a soil particle
Examples of habitats
pathogenic/symbiotic associations with plants/animals. Terrestrial (soil, sub surfaces), aquatic (fresh water, costal, deep sea)
Where and why is there extensive microbial growth
on surface of soil particles. Highly promoted in the rhizosphere because roots exude nutrients which microbes can absorb
What else can water content effect in the soil
oxygen levels. Waterlogged = low oxygen levels (anoxic)
Where is there the greatest microbial activity
in organic- rich soil surface layers (high nutrient availability). High nutrients especially around rhizosphere.
What is ground water
water in soils and rocks deep underground
Microbial life 3km into earth
chemolithotrophs, autotrophic bacteria and archaea found 3km deep. Must survive off nutrient poor diet and use H 2 as an electron donor for respiration
How does fresh water and marine aquatic habitats differ
salinity, barrage temperatures, depth and nutrient content
Fresh water aquatic environment
Highly variable in resources and conditions
Both oxygen consuming and oxygen producing organisms present
The balance controls the cycle of nutrients
Oxygenic phototrophs include algae and Cyanobacteria. Primary producers (energy comes from light). Planktonic (floating). Benthic (attached to the bottom of a lake/stream)
Habitat changes with depth
Costal and ocean water habitats
Very low nutrient levels, especially nitrogen, phosphorus and iron
Water temperatures are cooler and are more constant with seasons than freshwater
Overall mitochondrial numbers are lower in marine compared to freshwater
What sized cells are found in costal and ocean waters - why?
very small cells - requires less energy for cell maintenance
How are cells adapted to living in costal and ocean waters
require greater number of transport enzymes relative to cell volume to acquire nutrients from very dilute environments
Oxygenic photosynthesis in the ocean
major factor in controlling the earths carbon balance. Photic zone = wher elight can penetrate to. Oceans conatin largest microbial biomass
What are hydrothermal vents
underwater hit volcanic springs. Found 1000m to greater than 400m in depth
Abiotic growth factors
1.Nutrient availability
- Temperature
3.pH
4.Moisture
5.Oxygen
6.Pressure
7.Light
pH effects on microbial growth
Most microbes show a growth range of 2-3 units
Most natural environments have a pH between 4 and 9
Organisms optimised to this range are most common
What is optimal pH
measure of extra cellular environment. The intracellular pH must remain relatively close to neutrality
Is oxygen soluble in water
it is but poorly
Examples of anoxic (O2 free) environments
muds, bogs, marshes, waterlogged soil, intestinal tracts, sludge, sewage
What are facultive microoganisms
under appropriate nutrient conditions, they will grow under either oxic or anoxic conditions
What are microareophiles
aerobes that can only use O2 when its present at levels lower than air
What are aerotolerant microorganisms
anaerobic but can tolerate oxygen. However don’t use it in their metabolism
What is an extremophile
organism whose growth is dependent on extremes of temperature, salinity, pH, pressure or radiation which are generally inhospitable to most forms of life
Example of cold environments
oceans, the poles, glaciers
What is a psychrophile
optimal growth temperature is 15 degrees or lower. Max is 20 degrees. Found in constantly cold environments
What is a pyschromonas
sea ice bacterium - grows at 12 degrees - lowest known
What is pyscrotolerant bacteria
grows at 0 degrees. Optima is 20-40. Widely distributed. Found in temperature climates meat, diary, cider, veg
How are enzymes adapted for cold environments
optimal activity for low temperature. Contains more polar amino acids (fewer weak bonds). Secondary structure has a greater alpha helix, less beta pleated sheets to give protein greater flexibility
How are cell membranes adapted for cold environments
high content of unsaturated and shorter fatty acids, helping it to stay semifluid
What are cold shock proteins
maintain other proteins activity and bind specific mRNAs to facilitate their translation. Not limited to psychrophiles e.g. found in E.cook
What are cryoprotectants
solutes (e.g., glycerol) that help prevent the formation of ice crystals in the cell
Example of hot environments
surface soilds, compost heaps, hot springs (terrestrial, hydrothermal vents)
What are thermophiles
growth temperature optimum is greater than 45 degrees. Less extreme than the hyperthermophiles. Found in a range of habitats: edge of hot springs, soil surfaces etc…
What are hyperthermophiles
growth temperature optimum is greater than 80 degrees. Found in hot springs, only prokaryote. Growth rates often quite high(generation time as short as 1 hour) . Most heat tolerant example known as mentharapyus at 112 degrees.
What is a species gradient
As boiling water leaves hot springs it cools, creating a thermal gradient.
Different species grow at the different temperatures along the gradient.
What organisms can grow at higher temperatures
prokaryotes and non-phototropic organisms. archea most thermopjillic.
How are enzymes adapted for high temperatures
They are heat stable. Has critical amino acid substitutions at a few locations so it can fold in a heat-stable way. Contains more ionic bonds between basic/acidic amino acids. Often hydrophobic interiors
How has DNA stability increasesed for high temperatures
Increased cellular compatible solute levels - prevents chemical damage to DNA. Contains DNA gyrase. A species topioisomerase (only found in hyperthermophiles), introduces positive supercoils - more heat stable
How have membranes adapted to be more heat-stable
More staurated fatty acids, forms stronger hydrophobic environments, more long-chain fatty acids, have a higher melting point, have C40 hydrocarbons bonded to glycerol phosphate by ether link
What are acidophiles
microorganisms that grow best at pH 5.5 or below. Different classes are optimised to different pHs
What are alkaliphiles
Grow best at pH 8 or above. Found in environments such as soda lakes and high-carbonate soils.
What must cytoplasmic pH be
must stay near pH 7 to prevent destruction of macromolecules
What does optimal pH refer to
extracellular environment only
What does a high salt concentration do
males solute potential of the environment more negative. Osmotic gradient outside the cell so its harder to extract water from environment ‘physical drought’.
examples of high salt environemnts
sea water. dead sea, salt lake
What is a halophile
require NaCl for growth
What is halotolerant
can tolerate NaCl but grow best in absence of solute
How do cells prevent water leaving the cell to the hypertonic environment
Increase internal solute concentration using compatible solutes e.g., organic compounds which are highly soluble and dont interfere with cellular metabolism. Salt is too toxic
What can charged ions do
penetrate hydration shells of protein and interfere with non-covalent bonding. Neutrally charged ions do not penetrate hydration shells
