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Organisms And Their Environment > Microbiology > Flashcards

Microbiology Flashcards

1
Q

What did Robert Hooke do

A

wrote first book devoted to microscopic observations

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2
Q

What did Louis Pasteur do

A

disproved spontaneous generation by showing heat can be used to sterilise

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3
Q

What did Robert Koch

A

Microorganisms are often the cause of the disease. Developed Koch’s postulates by studying mice and anthrax and a disease caused by Bacillus anthacis.

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4
Q

Growing microorganisms

A

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

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5
Q

Why are tubes containing solid agar set on a slope

A

increases surface area, used for pure growth of a microorganism

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6
Q

Types of light microscopy

A

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)

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7
Q

Light microscope resolution

A

0.2 micrometres

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8
Q

Atomic force microscopy

A

measure forces between a probe and the atoms on the surface of the specimen, measures deviations from flat surface

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9
Q

Confocal laser scanning microscopy

A

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

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10
Q

Differential interface contrast microscopy

A

form of light microscopy, used polarised light (light in a single plane), cellular structures appear more 3D

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11
Q

Electron microsocopy

A

Uses electrons instead of visible light, electromagnets function as lenses, whole system operates in a vacuum

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12
Q

Transmission electron microscopy

A

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

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13
Q

Scanning electron microscope

A

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

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14
Q

Why study microbes

A

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

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15
Q

Archeae features

A

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

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16
Q

Protozoa features

A

Unicellular eukaryotes , Live in soil, wet sand, fresh and salt waters, Great diversity in shape, mobility and metabolism

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17
Q

Algae features

A

Eukaryotes ,Contain chloroplasts , Have cell walls, Both terrestrial and aquatic

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18
Q

What size do prokaryotic cells range from

A

0.2 micrometres to > 700 micrometres in diameter

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19
Q

What cells do eukaryotic cells range from

A

10 micrometres to > 200 micrometres in diameter

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20
Q

Why is a higher SA:V an advantage to small cells

A

faster nutrient exchange so they can grow faster and support a large population

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21
Q

Why is faster evolution an advantage to smaller cells

A

higher mutation rate (higher rate of cell division) which is a raw material for evolution allowing rapid adaptation to changing environments

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22
Q

What is the disadvantage to small cells

A

can only just fit in all the essential cellular components

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23
Q

What are endosporesz

A

highly differentiated cells, produced by certain species of bacteria, highly resistant to heat/harsh chemicals/ radiation, survival structures (like a nuclear bunker)

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24
Q

What is sporulation

A

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

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25
Q

Endospore structure

A

strongly refractive and impermeable to most dyes, usually seen as unstained regions within cells

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26
Q

Fimbriae and pilli composition

A

filamentous structures composed of protein extending from surface of a cell

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27
Q

What are fimbriae

A

enable cells to stick to surfaces and each other

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28
Q

What are instances where fimbriae exisist

A

salmonella species, neisseria gonorrhoeae, whooping cough

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29
Q

Pili features

A

longer than fimbriae but only 1 or 2 present. Best seen under electron microscope when coated with virus particles

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30
Q

What are the functions of pili

A

conjugation (genetic exchange between cells), adhesion of pathogens to specific host tissue and subsequent invasion, can be involved in motility

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31
Q

What is microbial locomotion

A

cells can move under their own power, enabling them to reach different parts of their own environment

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32
Q

What are taxis - microbial locomotion

A

movement towards something that will aid growth or away from toxins

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33
Q

Taxi examples

A

chemotaxis - response to chemicals. Phototaxis - response to light

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34
Q

Flagellum in aiding cell movement

A

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

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35
Q

What is polar flagellation

A

flagella are attached to one or both ends

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36
Q

What is a tuft of flagella

A

A group of flagella attached to one end of the cell

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37
Q

What is peritrichous flagella

A

Flagella inserted at many location

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38
Q

Flagella structure

A

helical, wavelength (distance between curves) is a characteristic for diff species, a molecular motor in the cell membrane drives rotation

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39
Q

Structure of flagellum molecular motor

A

Central rod, passes through a series of rings, mot proteins (act as stators). Rod and rings rotate while the mot proteins stay still

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40
Q

Where is the energy for rotation come from

A

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

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41
Q

How does the flagella change when there is an attractant present

A

there are longer runs and fewer tumbles

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42
Q

Gliding of cells

A

slower than swimming, cells must be in contact with a slid surface, colonies of gliding bacteria have distinct properties

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43
Q

Gliding mechanism - polysacchardie slime

A

connects cell surface with solid surface, as slime adheres to surface, the cell is pulled along

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44
Q

Gliding mechanism - twitching motility

A

repeated extension and retraction of type IV pili

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45
Q

What do myxobacteria form

A

multicellular structures - fruiting bodies

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46
Q

Features of fruiting bodies

A

often strikingly coloured and morphologically elaborate

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47
Q

What is the myxobacteria glide

A

Vegetative cells excrete slime to move across surface, leaves behind a slime trail

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48
Q

What is a myxobacteria swarm

A

slime trail is picked up by other bacteria, radiating pattern of established slime trails

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49
Q

Myxobacteria life cycle

A
  1. Myxospores are resistant resting cells released from sporangioles upon favourable conditions
  2. Myxospores germinate and form gram negative vegetative cells which divide to reproduce
  3. Vegetative myxobacteria are motile by gliding, forming visible slime trails
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50
Q

Myxobacteria life cycle 2

A
  1. Under favorable conditions, the vegetative cells swarm to central locations, forming an aggregation
  2. Aggregations of cells heap up into a mound, an early fruiting body
  3. Mounds of myxobacteria differentiate into a mature fruiting body, which produces myxospores packed within sporangles
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51
Q

What are the sources of carbon

A

eating something containing carbon or fixing your own

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52
Q

What is an autotroph

A

uses CO2 as their carbon source, primary producers, synthesise new organic matter

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53
Q

What is a heterotroph

A

uses organic compounds as their carbon source, either feed directly or on other cells or live off products other organisms excrete

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54
Q

What is a symbiotic relationship

A

cooperative relationship with the host

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55
Q

Parasitic relationship

A

antagonistic relationship with the host

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56
Q

Saprotrophic relationship

A

the host is dead

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57
Q

How do microbes get the energy they need to grow

A

chemical energy (chemotrophy) - organic (chemoorganotrophs) and inorganic (chemolithotrophs) and light energy (phototrophs)

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58
Q

Phototrophs - oxygenic photosynthesis

A

algae.green plants/cyanobacteria. CO2 into sugars. Light converts ADP into ATP. The reducing power is water to create oxygen

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59
Q

Phototrophs - anoxygenic photosythesis

A

purple and green bacteria. H2S is the reducing power creating SO4 2-. Light still used to convert ADP into ATP.

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60
Q

Chemoorganotrophs

A

oxidation of organic compounds releases energy stored as ATP can be aerobic or anaerobic

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61
Q

Chemoliphotrophs

A

oxidation of inorganic ions rleases ATP. Only in prokaryotes. e.g., sulphur and iron bacteria

62
Q

What is nitrogen fixing

A

converts atmospheric nitrogen gas into a form that can be used by cells

63
Q

Nitrogen fixation equation

A

N2 + 8H+ + 8e- –> 2NH3 + H2

64
Q

What are the 2 types of nitrogen fixing bacteria

A

free living (no host) and symbiotic

65
Q

Nitrogenase

A

catalyses nitrigen fixing. Made from dinitrogenase (contains iron and molybdenum, accepts electrons) and dinitrogenase reductase (contains iron and splits ATP)

66
Q

What is nitrification

A

oxidation of inorganic nitrogen compounds, preformed in nitrifying bacteria (found in soil/water)

67
Q

Nitrosomonas catalyse equation

A

2NH4+ + 3O2 –> 2NO2- + 4H+ + 2H2O

68
Q

Nitrobacter catalyses equation

A

2NO2- + O2 –> 2NO3-

69
Q

What is the importance of nitrogen fixation/ nitrification

A

part of plants productivity for sewage and waste treatments, removing toxic amines and ammonia

70
Q

What is growth in multicellular organisms compared to single cell

A

the whole organism gets bigger in multicellular, single cellular is increase in number of cells in population

71
Q

What is generation time

A

time taken for the cell to divide

71
Q

What is generation time

A

time taken for the cell to divide

72
Q

What are the steps of binary fission

A
  1. cell replicates its DNA
  2. The cytoplasmic membrane elongates separating DNA molecules
  3. Cross wall forms (septum) membrane invaginates
    4.Cross wall form completely
    5.aughter cells form
73
Q

How does generation time vary

A

Variable between and within species depending on nutritional and environmental factors e.g., temperature and the competition in a habitat

74
Q

What is a logarithmic scale

A

increases to the power of 10

75
Q

Generation time formula

A

time/number of generations in time (gradient)

76
Q

Final cell number formula

A

N2^n
N = initial cell number
n = number of generations during the period of exponential growth

77
Q

number of generations during the period of growth formula

A

(log(N)-log(N0))/ 0.301
N = final cell number
N0 = initial cell number

78
Q

What does exponential growth do

A

work in bases of 2 e.g., 2^6

79
Q

When does the lag phase occur

A

time between when culture is inncoulated into fresh media and significant growth

80
Q

What causes the length of the lag phase to vary

A

history of the inoculum, nature of the medium and growth conditions

81
Q

When does a longer lag phase occur

A

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

82
Q

What is the exponential phase

A

cells population doubles at regular intervals, the healthiest stsae

83
Q

What causes the exponential phase to vary

A

availability of environmental conditions (temperature, nutrients etc) and genetic characteristics of the organism

84
Q

What is the stationary phase

A

essential nutrient in culture medium runs out so waste products build up to toxic levels. Cell growth = cell death

85
Q

What is the death pahse

A

exponential decline of viable cells, rate of cell death > cell division. Viable cells remain in culture for long periods of time

86
Q

How to measure growth

A

microscopic counts, viable counts and spectrophometry

87
Q

How do you carry out a microscopic count

A

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

88
Q

Limitations of microscopic counts

A

Without special staining techniques, dead and live cells cannot be distinguished. Imprecise. Small cells difficult to see. Motile cells must be demobalised

89
Q

What is a viable cell

A

a cell that is able to divide and produce offspring

90
Q

What is the assumption made for viable counts

A

each viable cells will divide to form one colony

91
Q

How do you carry out a viable count

A

Pipette a sample on to agar and spread evenly using a sterile glass spreader. Count colonies

92
Q

Why is culture medium a source of error for viable counts

A

incubation conditions and incubation time have a big effect

93
Q

Why is culture medium a source of error for viable counts

A

incubation conditions and incubation time have a big effect

94
Q

may How is a mixed culture medium a limiting factor to viable counts

A

Not all cells grow at the same rate (different generation times), colony sizes may vary (miss small ones)

95
Q

Other limitations of viable counts

A

inaccurate pipetting, non-uniform sample (cell clumps), insufficient mixing, heat intolerance

96
Q

What is spectrophotometry

A

cells scatter light, turbidity can be used to estimate cell mass in a sample. More light scattering = more cell mass = more cells

97
Q

What is microbial ecology

A

a given species lives in certain places but not others - environments differ in their abilities to support diverse microbial populations

98
Q

What is an ecosystem

A

a dynamic complex of plants, animals and microbial communities and their non-living surroundings, which interact as a functional unit

99
Q

Microbes in an ecosystem

A

great metabolic diversity, primary catalysts of nutrient cycles, very important members of the ecosystem

100
Q

Why do microorganisms have microoenvironments

A

are very small so only directly experience a tiny local environment. Metabolic activities from microorganisms alter the conditions

101
Q

Why is diffusion important to microorganisms

A

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

102
Q

How is oxygen concentration measured

A

using micro electrodes in a soil particle

103
Q

Examples of habitats

A

pathogenic/symbiotic associations with plants/animals. Terrestrial (soil, sub surfaces), aquatic (fresh water, costal, deep sea)

104
Q

Where and why is there extensive microbial growth

A

on surface of soil particles. Highly promoted in the rhizosphere because roots exude nutrients which microbes can absorb

105
Q

What else can water content effect in the soil

A

oxygen levels. Waterlogged = low oxygen levels (anoxic)

106
Q

Where is there the greatest microbial activity

A

in organic- rich soil surface layers (high nutrient availability). High nutrients especially around rhizosphere.

107
Q

What is ground water

A

water in soils and rocks deep underground

108
Q

Microbial life 3km into earth

A

chemolithotrophs, autotrophic bacteria and archaea found 3km deep. Must survive off nutrient poor diet and use H 2 as an electron donor for respiration

109
Q

How does fresh water and marine aquatic habitats differ

A

salinity, barrage temperatures, depth and nutrient content

110
Q

Fresh water aquatic environment

A

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

111
Q

Costal and ocean water habitats

A

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

112
Q

What sized cells are found in costal and ocean waters - why?

A

very small cells - requires less energy for cell maintenance

113
Q

How are cells adapted to living in costal and ocean waters

A

require greater number of transport enzymes relative to cell volume to acquire nutrients from very dilute environments

114
Q

Oxygenic photosynthesis in the ocean

A

major factor in controlling the earths carbon balance. Photic zone = wher elight can penetrate to. Oceans conatin largest microbial biomass

115
Q

What are hydrothermal vents

A

underwater hit volcanic springs. Found 1000m to greater than 400m in depth

116
Q

Abiotic growth factors

A

1.Nutrient availability

  1. Temperature

3.pH

4.Moisture

5.Oxygen

6.Pressure

7.Light

117
Q

pH effects on microbial growth

A

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

118
Q

What is optimal pH

A

measure of extra cellular environment. The intracellular pH must remain relatively close to neutrality

119
Q

Is oxygen soluble in water

A

it is but poorly

120
Q

Examples of anoxic (O2 free) environments

A

muds, bogs, marshes, waterlogged soil, intestinal tracts, sludge, sewage

121
Q

What are facultive microoganisms

A

under appropriate nutrient conditions, they will grow under either oxic or anoxic conditions

122
Q

What are microareophiles

A

aerobes that can only use O2 when its present at levels lower than air

123
Q

What are aerotolerant microorganisms

A

anaerobic but can tolerate oxygen. However don’t use it in their metabolism

124
Q

What is an extremophile

A

organism whose growth is dependent on extremes of temperature, salinity, pH, pressure or radiation which are generally inhospitable to most forms of life

125
Q

Example of cold environments

A

oceans, the poles, glaciers

126
Q

What is a psychrophile

A

optimal growth temperature is 15 degrees or lower. Max is 20 degrees. Found in constantly cold environments

127
Q

What is a pyschromonas

A

sea ice bacterium - grows at 12 degrees - lowest known

128
Q

What is pyscrotolerant bacteria

A

grows at 0 degrees. Optima is 20-40. Widely distributed. Found in temperature climates meat, diary, cider, veg

129
Q

How are enzymes adapted for cold environments

A

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

130
Q

How are cell membranes adapted for cold environments

A

high content of unsaturated and shorter fatty acids, helping it to stay semifluid

131
Q

What are cold shock proteins

A

maintain other proteins activity and bind specific mRNAs to facilitate their translation. Not limited to psychrophiles e.g. found in E.cook

132
Q

What are cryoprotectants

A

solutes (e.g., glycerol) that help prevent the formation of ice crystals in the cell

133
Q

Example of hot environments

A

surface soilds, compost heaps, hot springs (terrestrial, hydrothermal vents)

134
Q

What are thermophiles

A

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…

135
Q

What are hyperthermophiles

A

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.

136
Q

What is a species gradient

A

As boiling water leaves hot springs it cools, creating a thermal gradient.

Different species grow at the different temperatures along the gradient.

137
Q

What organisms can grow at higher temperatures

A

prokaryotes and non-phototropic organisms. archea most thermopjillic.

138
Q

How are enzymes adapted for high temperatures

A

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

139
Q

How has DNA stability increasesed for high temperatures

A

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

140
Q

How have membranes adapted to be more heat-stable

A

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

141
Q

What are acidophiles

A

microorganisms that grow best at pH 5.5 or below. Different classes are optimised to different pHs

142
Q

What are alkaliphiles

A

Grow best at pH 8 or above. Found in environments such as soda lakes and high-carbonate soils.

143
Q

What must cytoplasmic pH be

A

must stay near pH 7 to prevent destruction of macromolecules

144
Q

What does optimal pH refer to

A

extracellular environment only

145
Q

What does a high salt concentration do

A

males solute potential of the environment more negative. Osmotic gradient outside the cell so its harder to extract water from environment ‘physical drought’.

146
Q

examples of high salt environemnts

A

sea water. dead sea, salt lake

147
Q

What is a halophile

A

require NaCl for growth

148
Q

What is halotolerant

A

can tolerate NaCl but grow best in absence of solute

149
Q

How do cells prevent water leaving the cell to the hypertonic environment

A

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

150
Q

What can charged ions do

A

penetrate hydration shells of protein and interfere with non-covalent bonding. Neutrally charged ions do not penetrate hydration shells

Organisms And Their Environment (9 decks)

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