block A- general microbiology Flashcards
1
Q
name different types of microorganisms?
A
bacteria
fungi
viruses
2
Q
why are microorganisms improtant?
A
the production of food and drinks
decomposition of organic matter
the maintenance of the earths ecosystem
theyre vital in human health - both causing and helping
3
Q
what can understanding microorganisms’ biology and behaviour help with?
A
its essential for the development of new medical treatments
improvement of food safety
the management of enviromental resources
4
Q
what is the oldest form of life?
A
microorganisms
5
Q
what are stromatolites?
A
theyre fossilized stromatolites with are layered structures formed by the growth of microbial communities
theyre were formed about 3.5 billion years ago
6
Q
how long ago was it thought that the first microorganisms emerged?
A
about 3.5-4 billion years ago
7
Q
where were the first fossils found?
A
greenland
8
Q
what makes up the largest mass of living material on earth?
A
microorganisms
9
Q
how much living mass material is there on the world and how many times bigger than all the rest of the living material on the planet?
A
around 5 x 10^30 grams is the mass of all the bacteria found in the world
thats 2.5x the rest of the living material on the world
10
Q
where is most of the biomass found?
A
its mostly found in the ocean and in the soil
11
Q
what is the carbon cycle?
A
its the decomposition of organic matter which releases CO2 through respiration - i think microbes play a massive part in this cycle
12
Q
what is the nitrogen cycle?
A
its a cycle that concerts nitrogen gas into forms that plants and animals can use like ammonia, nitrate and nitrile
its actually called nitrogen fixation and is essential for the growth of plants and the survival of many animals
13
Q
what happens if the soil becomes depleted in nitrogen?
A
theres a break in productivity
14
Q
what are some of the major processes which are part of biogeochemical cylcles that microbes help with?
A
the carbon cycle, the nitrogen cycle, sulpher cycle, phospherous cycle and iron cycle
15
Q
what is the sulpher cycle?
A
some microorganisms can oxidise sulpher compounds like hydrogen sulphide and convert it into sulphuric acid
this process plays a critical role in the geochemical cycling of sulpher and the formation of sulpher minerals
16
Q
what is the phosphorous cycle?
A
its involved in the release of phosphate from minerals which is an essential nutrient for plants and animals
they also play a role in the formation of bones and teeth by converting phosphates into hydroxyapatite
17
Q
what is the iron cycle?
A
some microorganisms can oxidise iron compounds such as ferrous iron and convert them into ferric iron
this process plays a critical role in the geochemical cycling of iron and the formation of iron minerals
18
Q
what extremes can microorganisms survive in?
A
high temperatures
low temperatures
high pressure
high salinities
high radiation
high acidity
19
Q
what types of bacteria can survive at hogh temperatures?
A
thermophiles and hyperthermophiles
these can survive at temps as high as 80 degrees
theyre found in volcanic hot springs, guysers and deep-sea hydrothermal vents and subsurface oil resivoirs
20
Q
what types of microorganisms can survive at high pressures? and where are they found?
A
piezophils can survive and grow at pressures as high as 1800x atmospheric pressures
theyre found in subsurface oil resivoirs and deep-sea hydrothermal vents
21
Q
what types of microorganisms can survive at high salt concentrations and where are they found?
A
hapophils - theyre found in salt flats and salt mines
22
Q
what types of microorganisms survive at high radiation and where are they found?
A
deinococcus radiodurans can survive and grow in inviroments with hoigh levels of radiation like nuclear waste sites
23
Q
what types of microorganisms survive in high acidity habitats and where are they found?
A
acidophils
theyre found in acid mine drainage, acid hot springs and acid soils
24
Q
what microorganisms are needed in symbiosis in some plant species?
And what do they do?
A
rhizobia
these live in the roots and convert atmospheric nitrogen into a form that plants can use
this is essential for the growth of plants
25
how do microorganisms live in symbiosis with animals?
microorganisms digest their food
e.g. ruminant microbes break down plant material and terminte microbes digest wood
26
how do microorganisms live in symbiosis with humans?
the gut microbiome is important for digestion, metabolism, immunity and the production of vitamins and other essential compounds
27
how does marine life live in symbiosis with microorganisms?
microorganisms are responsible for most primary production, this is the process of converting dissolved inorganic compounds into organic compounds
these form the basis of the oceanic food web
they also play an important role in the cycling of nutrients like carbon, nitrogen and phospherous
28
how do microorganisms help in the soil?
they breakdown dead plants and animals to release nutrients back into the soil
they also help to maintain the soil structure by forming microbial aggregates which help to retain the water and air
29
what are the main characteristics of microbial cells?
prokaryotes
- they have no membrane enclosed organelles with no nucleus
- generally smaller than eukaryotic cells
archaea and bacteria-
- DNA is enclosed in a membrane bound nucleus
- cells are generally larger and more complex
- contain organelles
30
what are the characteristics of wukaryotic cells?
- their DNA is linear and found in the nucelus
- theyre assiciated with proteins that help in the folding of DNA
- mitochondria are thought to have arisen from bacteria
- they usually have more than one chromosome, with generally 2 copies of each chromosome
- during cell division, the nuclus divides by mitosis
- during sexual reproduction, the genome is halfed by meiosis
31
what are the characteristics of prokaryotic cells?
they generally have a single, circular DNA molecule called a chromosome
the DNA aggragates to form the nucleoid region
prokaryotes also may have small amounts of extrachromosomal DNA called plasmids that confer special properties
32
what is the adaptive advantage to do woth plasmids?
the prokaryotes can swap plasmids, this causes a massive problem related to antibiotic resistance
33
how much bigger is the human genome compared to e. coli - the amount of DNA per cell and the number of genes?
humans have 1000x more DNA per cell and 7x more genes than E coli
34
what does metabolism mean?
chemical transformation of nutrients
35
what does reproduction mean?
generation of two cells from one
36
what does differentiation mean?
synthesis of new substances or structures that modify the cell (only in some microbes)
37
what does communication mean?
the generation of, and response to, chemical signals (only in some microbes)
38
what does movement mean?
via self-propulsion, many forms of it in microbes
39
what does evolution mean?
genetic changes in cells that are transferred to the offspring
its the process of chnage over time that results in new varieties and species of organisms
40
what is phylogeny?
its the evolutionary relationship between organisms
relationships can be deduced by comparing genetic information in the diffeent specimens
rRNA is excellent for determining phylogeny
relationships visualised on a phylogenetic tree
41
how can you assess evolution by phylogeny?
you can look at the same gene across different microbes and compare the simialrity and difference of a few genes picked out from the whole genome
42
what are the three distinct lineages of cells called domains?
bacteria
archaea
eukarya
43
how did evolution proceed from the last universal common ancestor?
it proceeded to form two domains- bacteria and archaea- then archaea leater diverged to form two domains- archaea and eukarya
44
what are evolutionary relationships displayed on?
phylogenetic tree
45
what does habitat mean?
its the environment in which a microbial population lives
46
what does microbial community mean?
its when microbes exist in nature in populations of interacting assemblages
47
what does ecosystem mean?
this refers to all living organisms and physical and chemical constituents of their environment
48
what is microbial ecology?
its the study of microbes in their natural enviroment
49
what is diversity and abundances of microbes controlled by?
resources (nutrients) and enviromental conditions (temp, pH and O2)
50
what can the activities of microbial communities affect?
they can affect the chemical and physical properties of their environment
- ecosystems are greatly influenced by microbial activities
- microorganisms change the chemical and physical properties of their habitats through their activities for example, the removal of nutrients from the envirmoment and the excretion of waste
51
are microbes typically more harmful or beneficial?
there is many more benifitial ones compared to harmful
52
what are the positive effects on agriculture by microorganisms?
nitrogen-fixing bacteria
cellulose-degrading microbes in the rumen
regeneration of mutrients in soil and water
53
what are the negative impacts of microorganisms on agriculture?
they cause diseases in plants and animals
54
what are the negative effects caused by microorganisms on food?
they can cause food spoilage- for many foods so methods of preservation are needed
55
what are the positive imapcts of microorganisms on food?
microbial transformations - typically fermentations
- dairy products (cheese, yogurt and buttermilk)
- other food products (sauerkraut, pickles, leavened bread and beer)
56
how do microorganisms help in energy and the enviroment?
they help produce biofuels like methane, ethanol and hydrogen
they also help clean up pollutants (bioremeduation)
57
how do microorganisms help in energy and in the environment?
exploitation of microbes for the production of antibiotics, enzymes and various chemicals
genetic engineering of microbes to generate products of value to humans, such as insulin
58
who are influential figures involved in the discovery of microorganisms?
robert hooke- first to describe microbes
antoni van leeuwenhoek - the first to describe bacteria
ferdinand cohn - founded the feild of bacterial classification and discovered bacterial endospores
59
what did louis pasteur do?
- discovered that living organisms discriminate between optical isomers
- discovered that alcoholic fermentation was a biologically mediated process
- disproved theory of spontaneous generation- this lead to the development of methods for controlling the growth of microorganisms
- developed vaccines for anthrax, fowl cholera and rabies
60
what did koch do?
Robert Koch (1843–1910)
Demonstrated the link between microbes and infectious diseases
Identified causative agents of anthrax and tuberculosis
Koch's postulates (Figure 1.20)
Developed techniques (solid media) for obtaining pure cultures of microbes, some still in existence today
Awarded Nobel Prize for Physiology and Medicine in 1905
61
what is the central dogma of molecular biology?
replication, transcription and translation
62
what is supercoiled DNA?
the DNA is further twisted to save space
63
what are positive and negative supercoiling of the DNA?
(Not the positives and negatives of supercoiling)
negative- the double helix is underwound
positive - the double helix is overwound
64
what is relaxed DNA?
the DNA has a number of turns predicted by number of base pairs
negative supercoiling is predominantly found in nature
65
what does DNA gyrase do?
it introduces supercoils into DNA
this is an enzyme that packs the DNA, if you inhibit the enzyme, the cell will stop growing
66
what do you have to do to one of the strands so it can become supercoiled?
you have to cut one of the strands then it can become super coiled
67
what does the DNA gyrase so to DNA supercoiling?
it catalyses the DNA supercoiling
68
what is a chromosome?
its arge and encodes all the essential genes and more
69
what is a plasmid?
small, many copies, non-essential bt advantageous genes (e.g. antibiotic resistance)
70
what are transposable elements?
segment of DNA that can move from one site to another site on the same or different DNA molecule
theyre inserted into three main types- insertion sequences, transposes and special viruses
71
what are characteristics of plasmids?
they replicate seperately from the chromosome
the majority of them are double stranded
most are circular
they're normally beneficial for the cell
they're not extracellular
some can auto replicate
its expendable and usually doesnt have genes for growth under all conditions
72
what are some of the characteristics of chromosomes?
they're genetic elements with housekeeping genes
the presence of genes is necessary for genetic element for it to be called a chromosome
73
what type of bacterium are 70% of antibiotics made up of?
streptomyces
74
what does a genetic element have to have to be called a chromosome?
the presence of genes
75
what do sigma factors recognise?
they recognise 2 highly conserved regions of the promoter
theyre called the 'pribnow box' and the '-35 region'
76
where is the pribnow box located?
10 bases before the start of transcription (-10 region)
77
where is the -35 region located?
~35 bases upstream of transcription
78
what factors govern promoter recognition of RNAP?
sigma factors
79
what does polycistronic mean?
it means that multiple proteins can be coded form one mRNA
80
what is a unit of transcription?
its the unit of chromosome bounded by sites where transcription of DNA to RNA is initiated and terminated
81
what are the 3 types of rRNA?
16S
23S
5S
82
how long are mRNA half lives?
only a few mins
83
what is a polyextronic mRNA molecule?
an mRNA encoding a group of co-transcribed genes
84
are RNA polymerases the same in the three domains of life?
no, theyve all got slightly different structures and subunits
eukaryotes have diffrent types of RNA polymerases but bacteria and eukaryotes only have one type each
85
how is gene expression regulated?
its regulated in the form of activation and repression
it takes place before the initiation site
86
what are homodimeric proteins?
they're proteins composed of two identical polypeptides
87
what do protein dimers ineract with?
inverted repeats on DNA
88
how does the short half life of mRNA help the cell?
it prevents the production of unneeded proteins
89
what does the regulation of transcription usulally require?
proteins that can bind to DNA
90
what are the different outcomes that are possible after DNA binding?
1. DNA binding protein may catalyse a specific reaction on the DNA molecule
2. the binding event can block transcription (negative regulation)
3. the binding event can activate transcription (positive regulation)
91
what is an inducer?
its a substance that induces enzyme synthesis
92
what is a co-repressor?
its a substance that represses enzyme synthesis
93
what do effectors mean?
its the collective name for inducers and repressors
94
what is an operon?
its a cluster of genes arranged in a linear fashion whose expression is under control of a single operator
95
what is the operator and what binds to it?
its located downstream of the promoter and transcription is physically blocked when the repressor binds to the operator
96
what can enzyme induction be controlled by?
repressors and inducers
97
what does the addition if the inducer do to transcription?
it inactivates the repressor and transcription proceeds
98
what type of control is a repressor part of?
negative control
99
what is a repressor's role?
its inhibitory
100
what is negative control?
its a regulatory mechanism that stops transcription
101
what is repression?
its preventing the synthesis of an enzyme in response to a signal
enzymes affected by repression make up a small fraction of total proteins
this typically affects anabolic enzymes
102
how does enzyme inhibition in the arginine operon work?
if arginine is present in the external environment - it binds to the repressor and blocks the transcription of the synthesis of arginine
if arginine is not present - arginine synthesis isn't inhibited and the cell can make its own arginine
103
what is induction?
- its the production of an enzyme in response to a signal
this typically affects catabolic enzymes like the lac operon
enzymes are then synthesised only when they're needed
these enzymes are only made when theyre needed so that no energy is wasted
104
what happens in enzyme induction in the lactose operon if there isn't any lactose ?
this is the gene that the cell uses to catalyse the lactose
if there isnt any lactose then transcription is blocked because the repressor isnt blocked
105
what is positive control?
regulator protein activated the binding of RNA polymerase to DNA
106
what happens in maltose catabolism in E, coli?
maltose activator protein cant bind to DNA unless it first binds maltose
maltose operon is responsible to produce the gene so the cell can use the maltose
if there isnt any maltose then the activator protein doesnt bind to the activator binding site and theres no transcription of the gene
activator proteins bind specifically to certian DNA sequences called activator binding site
107
what is the activator binding site?
its a specific site where activator proteins bind specifically to certain DNA sequences
108
how do promoters of positively controlled operons bind to RNA polymerase?
they bind weakly
109
how close/ far can the activator binding site be from the promoter?
it could be very bear it or kilobases away, if its kilobases away, it could bend the DNA
110
what may activator proteins do when they help RNA polyerase recognise the promoter?
they may cause a change in the DNA structure or may interact directly with RNA polymerase
111
where are the genes for maltose?
theyre spread out acctoss the chromosome in several operons
112
what does each operon have?
an activator binding site
113
what is a regulon?
its where multiple operons are controlled by the same regulatory protein
they also exist for negatively controlled systems
114
what are global control systems?
regulate expression of many different genes simultaneously
115
what is an example of global control?
catabolite repression
synthesis of unrelated catabolic enzymes is repressed if glucose is present in growth medium
lac operon is under contorl of catabloite repression
this ensures that the best carbon and energy source is used first
116
what is diauxic growth?
its two exponential growth phases
117
what is transcription controlled by in catabolite repression?
its controlled by an activator protein and is a form of positive control
118
what type of molecule is cyclic AMP and what is it derived from?
its derived form a nucleic acid precursor and is a regulatory nucleotide
119
what does CRP stand for?
cyclic AMP recpetor protein and its an activator protein
120
how many catabolic operons are affected by catabolite repression?
dozens
enzymes for degrading lactose, maltose ans other common carbon sources
121
what are flagellar proteins controlled by?
catabolite repression
this means that the flagella dont have to swim in search of nutrients
122
explain the basis of catabolite repression?
- the operon is off when glucose and lactose are present
- when neither is present, the repressor is bound
- when only glucose is present, the operon is off because the lac repressor is bound and because CAP isnt bound
- when only lactose is bound, the operon is on
123
the more regulation there is, the what?
the better you can fine tune the process
124
how can prokaryotes regulate cellular metabolism in response to environmental fluctuations?
external signals are transmitted directly to the target
125
what is signal transduction?
its when external signals are detected by a sensor and transmitted to the regulatory machinery
126
what types of systems are most signal transduction systems?
two-component regulatory systems
127
what 2 different proteins make up the two component regulatory system?
sensor kinase- this is in the cytoplasmic membrane and detects environmental signal and auto phosphorylates
response regulator- this is in the cytoplasm and is a DNA binding protein that regulates transcription
128
what auto-phosphorylates the receptor kinase?
the enviromental signal
129
what is the role of the feedback loop in two-component reguatory systems?
to terminate the signal
130
how many two-component systems are there in E. coli?
almost 50
131
what are some examples of two-component systems in E. coli?
phosphate assimilation
nitrogen metabolism
osmotic pressure response
132
do archaea have two component regulatory systems?
yeah, some do
133
do some signal transduction systems have multiple regulatory elements?
yeah
134
what are modified two-component systems used in chemotaxis?
they sense temporal changes in attractants or repellents
regulate flagellar rotation
135
what are the 3 main steps of the regulation of chemotaxis?
1. response to signal
2. controlling flagellar rotation
3. adaptation
136
what is involved in the 'response to signal' step of regulation of chemotaxis?
sensory proteins in cytoplasmic membrane sense attractants and repellents
methyl-accepting chemotaxis proteins (MCPs) bind attractant or repellent and initiate flagellar rotation
137
what is involved in the 'controlling flagellar rotation' step of the regulation of chemotaxis?
controlled by CheY protein
this results in counterclockwise rotation and runs
CheY-P results in clockwise rotation and tumbling
138
what happens in the 'adaptation' step of regulation of chemotaxis?
feedback loop- this allows the system to reset and continue to sense the presence of a signal
this involves modifications of MCPs
139
what are photsotaxis?
movement towards light
the light sensor replaces MCPs
140
what are aerotaxis?
movement towards oxygen
redox protein monitors oxygen levels
141
what is quorum sensing?
its the mechanism by which bacteria assess their population density
142
what does quorum sensing ensure?
it ensures that there's a sufficient number of cells that are present before initiating a response that, to be effective, requires a certain cell density like toxin production in pathogenic bacteria
143
each species of bacteria produces a specific autoinducer molecule, what do these do?
they diffuse freely accross the cell envolope and reach high concentrations inside the cell only if many cells are near
binds to specific activator protein and triggers transcription of specific genes
144
what is acyl homoserine lactone (AHL)?
its a hormone of bacteria and they produce more and more until quorum is reached, this is the certian density of cells to switch on transcription of genes, its the density of population
145
what operon encodes bioluminescence?
lux operon
146
what is quorum sensing present in?
likely archaea
some microbial eukaryotes
147
what are examples of quorum sensing?
virulence factors
switching from free-living to growing as a biofilm
148
what are the stages of biofilm formation?
increasing cell population
production of AHLs and c-di-GMP which leads to expolysaccharide production and flagella synthesis
attachment
mature biofilm
149
what happens in biofilm formation?
produces polysaccharides that increase pathogenicity and antibiotic resistance
two quorum-sensing systems
produces AHLs and cyclic di-guanosine monophosphate (c-di-GMP)
150
what does bioflim protect against?
everything, they are very strong and are produced by quorum sensing
151
what is the typical soil bacteria size?
0.3 x 0.5um
152
what is the typical marine bacteria size?
0.3 x 1 um
153
what is the typical size of Escherichia coli?
1 x 3 um
154
what are the exceptions to the tiny size of microbes?
Epulopiscium fishelsoni - 50 × 600 µm
Thiomargarita namibiensis - 750 µm
155
what is the small cell size used to cope with in prokaryotes?
its a way to cope with low substrate availability, this increases the surface area to volumw ratio
substrate uptake is via cell membrane proteins
increasing surface area/ volume ratio improves the avalability to supply nutrients to the cytoplasmic volume
156
what are various cell shapes of microbes and give examples of some?
Spherical (coccus) e.g. Micrococcus luteus
Rod (bacillus) e.g. Bacillus subtilis
Comma (spirilla) e.g. Vibrio cholera
Corkscrew (spirochetes) e.g. Borrelia burgdorferi
Appendaged e.g. Caulobacter crescentus
Filamentous e.g. some cyanobacteria
157
what microbial habitats can microbes live in?
almost anywhere with water
temperature -10 to 121 degrees
pH 0-11
NaCl : 0 to 6M (~saturation)
others: oxygen, pressure and radiation
158
what extremes can microbes live in?
extremes in temp, pH, salt, dessication, radiation and pressure
159
why do microbes have diverse metabolic strategies?
because they're usually competing with other microbes for resources/ survival
160
what is a xerophile?
bacteria that can survive without much water
161
what are psychrophile?
theyre microbes that can survive in extreme cold temperatures?
162
what are thermophiles?
theyre microbes that can survive in extreme hot temperatures
163
what are microbes called that can live in extremes of pH (theres different words for high and low pH)?
acidophils and alkaliphiles
164
what are salt-loving microbes called?
halophiles
165
what are bacteria that can survive in high NaCl conccentrations?
halotolerant
166
what are microbes that live deep in the ocean who can survive high pressures called?
barophiles
167
organisms can be facultive and obligate - what does that mean?
facultive- makes things easier for others
obligate - restricted to a particular function
168
what are the three cardinal temperatures?
minimum
optimum
maximum
169
what is involved in bateria comminuites with inter- and intra- species?
cell-cell signalling
community behaviour, division of labour, 'altruism'
can have complex differentiation
metabolism
- because they are relatively small bacteria often work cooperatively to have an effect on their environment
they live in complex, changing environments
170
what is mutualism?
its when the host benefits and the microbes benefit from their association
171
what does pathogenesis mean?
the microbes cause harm to their host
172
what does anabaena do?
they produce O2 and have a key role in the environment
173
what do microbes need?
sufficient energy sources and anabolic raw materials - mainly C, N, S and P
you also need some 'trace elements'- certian elements, metal ions and vitamins are used as enzyme co-factors
iron is extremely important for pathogenic bacteria
Fe is limiting in blood/ tissue becuase its bound
bacteria use sideophores to capture iron
174
what are photophils?
photosynthetic - energy from sunlight
175
what are chemotrophils?
energy from oxidation of chemicals
theyre sometimes distinguished as: chemo-litho-trophs which get energy from oxidation of inorganic chemicals hydrogen sulphide, sulpher, ammonia, nitrates, hydrogen gas or iron
chemo-organo-trophs which gets energy from oxidation of organic chemicals
176
what are the two categories of organisms?
autotrophic- they make their own food
heterotrophic - food from other sources
177
what are the two names for microbes that can and cannot fix CO2?
ones that can- autotrophs
ones that cant - heterotroph
178
what is oligotrophy?
its the rule in nature
most of the biosphere has low availability of nutrients
olgiotrophy = small feeding and is growth at low nutrient concentrations
179
what are photoautotrophs?
Cyanobacteria:
Use hydrogen atoms from water to reduce carbon dioxide to form carbohydrates
Produce oxygen gas (oxygenic process)
First organisms to conduct oxygenic photosynthesis (generated atmospheric O2)
Significant proportion of marine plankton (and marine microbial food web)
180
what are lichens and what do they do?
Lichens: an association between two partners: an ascomycete (fungus) and a cyanobacterium
Cyanobacteria provide organic compounds via photosynthesis, and can fix nitrogen
Fungus provides protection, water retention, extracts minerals and nutrients from substrate
Sometimes a third partner (basidiomycetous yeast) – Spribille et al 2016
181
what are chemoautototrophs?
they fix CO2 to make organic compounds, obtain energy from (usually inorganic) chemicals
182
what happens in the nitrification in natural enviroments?
Central role in global nitrogen cycle
Loss of ammonia-based fertilisers
Nitrate pollution
N removal in wastewater treatment
Competition with primary producers for ammonia
Corrosion of buildings
Production of greenhouse gases
Biodegradation of organic pollutants
183
what are photohetertrophs?
example - halobacteria
Halobacteria possess the protein Bacteriorhodopsin
Light energy is used to transfer protons across the membrane out of the cell.
The resulting proton gradient is used to
generate ATP
Gives Halobacteria their distinctive colour
Cannot fix CO2
Use organic carbon
184
what are chemoheterotrophs?
Probably the most common nutritional mode
Uses organic (carbon) compounds for both carbon requirement and energy generation
Most bacterial pathogens are chemoheterotrophs
185
what has more metabolic diversity- archaea and bacteria or eukaryotes?
archaea and bacteria
