1
Q
what did Holger Jannasch discover
A
- unculturable marine bacteria
- decomposition of material in the depths of the ocean takes 100x longer than on land
2
Q
what will you find where there are rich sources of carbon in not hot undersea oases
A
life!
- cold seeps
- whale fall
- shipwrecks
3
Q
true or false: most life forms around hydrothermal vents require sunlight for survival
A
true
4
Q
what is eutrophication
A
- oxygen dead zone
- excessive richness of nutrients in a lake or other body of water, frequently due to runoff from the land, which causes a dense growth of plant life and death of animal life from lack of oxygen.
5
Q
what do all species of bacteria have a need for?
A
nitrogen and phosphorous
6
Q
anoxic
A
water without oxygen
7
Q
what is soil?
A
- complex mixture of decaying organic and mineral material
- life support for vast # of microbes, as well as terrestrial plants
8
Q
what is in the organic horizon and what decomposes it
A
leaf litter, organic matter, top layer
decomposed by fungi, actibonmyctes, slime molds
9
Q
what is in the aerated horizon?
A
decomposed organic particles and minerals
10
Q
what is in the elutriated horizon?
A
insoluble particles
11
Q
what is in the B horizon?
A
clay and minerals
12
Q
which agricultural practice would be most harmful to soil microbes?
a) applying drainage to poorly drained soil
b) application of sewage sludge
c) driving over the soil with heavy equipment
d) application of manufactured fertilizer pellets
e) application of raw barnyard manure
A
d) application of manufactured fertilizer pellets
13
Q
what are the levels of soil?
A
- organic horizon
- aerated horizon
- elutriated horizon
- B horizon
- water table
- water-saturated horizon
- bedrock
14
Q
what do roots from plants secrete in soil?
A
polysaccharides
15
Q
true of false: a soil particle supports a lot of microbe life
A
true
16
Q
what is streptomyces?
A
- a major genus of soil bacteria
- notable for the antibiotics they make
- responsible for smell of soil
17
Q
what are nematodes?
A
microscopic works that reside in the top 15cm of the soil
18
Q
what do microbes in the rhizosphere do?
A
- help proest plants from pathogens
- may fix nitrogen
- feed off nutrients provided by plant
19
Q
what are endomycorrhizae?
A
- fungi that invade the root cell
- form arbuscules
- completely dependent on host, can’t sexually reproduce
20
Q
how do endophytes grow?
A
within plant tissue
21
Q
what are the 3 domains of life?
A
eukarya
bacteria
archaea
22
Q
what are the 2 kingdoms of unicellular organisms?
A
bacteria
archaea
23
Q
what are the 2 kingdoms of multicellular organisms?
A
plants
animals (including fungi)
24
Q
what is the kingdom made of both unicellular and multicellular organisms?
A
protists (including algae)
25
what are the 8 functions of life?
```
respiration
regulation
reproduction
excretion
growth
nutrition
transport
synthesis
```
26
what are carbohydrates building blocks?
monosaccarides
27
what are proteins building blocks?
amino acids
28
what are nucleic acids building blocks?
nucleotides
29
what are lipids building blocks?
glycerol
| fatty acids
30
what is life on Earth made from?
stardust: remnants of supernovae
31
what does life require?
- continual imputes of energy
| - temperature range the permits liquid water
32
how did ER and nuclear envelope of eukaryotes evolve?
from infoldings of the plasma membrane in a primordial cell
33
how does mitochondrion produce energy?
from chemical components
34
how does chloroplast produce energy?
from chemical components
35
what did Robert Hooke do?
- built first microscope
| - coined term cell
36
what did Antonie Van Leeuwenhoek do?
1st person to observe single celled organism
37
what did Edward Jenner do?
introduced vaccination against small pox
38
how was small pox vaccination created?
developed from cowpox scab
39
what did Lazzaro Spallanzani do?
1st to show that broth sterilized failed to grow microbes
40
what did Louis Pasteur do?
- discovered fermentative metabolism
| - Used swan-necked flasks to demonstrate that microbes are not produced through spontaneous generation
41
what did Florence Nightingale do?
- founder of medical epidemiology
- Demonstrated that infection caused more morbidity than any other condition during the Crimean War
- Persuaded the British Army to adopt more hygienic conditions to counteract infection
42
what did Robert Koch do?
- 1st to determine specific microbes cause specific diseases
| - developed Koch's postulates
43
what did Angelina and Walter Hesse do?
1st to use slid medium to culture microbes
44
what did Ignaz Semmelweis do?
1st proponent of hand-washing as an important process for physicians in hospitals
45
what did Joseph Lister do?
Pioneered the use of a clean (free-from microbes) operating area for his patient
46
who was involved in the discovery of viruses?
Dmitry Ivanovsky
Martinus Beijerinick
Wendell Stanley
47
according to the 3 domain model of classification, the ancestors of mitochondria are:
a. cyanobacteria
b. fungi
c. proteobacteria
d. archaea
e. protocista
c. proteobacteria
48
analysis of 165 rRNA gene sequence showed that
a. plants and animals are as distant from bacteria as they are to each other
b. all microbes are only distinctly related to the eukaryotes
c. Achaea are almost as distant from bacteria as they are from eukaryotes
d. viruses are closely related to prokaryotes
c. Achaea are almost as distant from bacteria as they are from eukaryotes
49
a photosynthetic organism that utilizes inorganic iron as an electron source and fixes its own carbon would be called:
a. photolithoautotroph
b. photochemoheterotroph
c. photolithoheterotroph
d. chemolithoheterotroph
e. chemolithoautotroph
a. photolithoautotroph
50
which of the following consists of prokaryotic cells:
a. bacteria and fungi
b. archaea and fungi
c. viruses and bacteria
d. bacteria and archaea
e. archaea and viruses
d. bacteria and archaea
51
which of the following statements is false regarding archaea:
a. some archaea were originally wrongly identified as bacteria
b. archaea does not use fatty acids to build their membrane phospholipids
c. all methanogens are archaea
d. all archaea possess pseudopeptidoglycan
e. S-layers are very common in many archaea species
d. all archaea possess pseudopeptidoglycan
52
which is our closest relative in this group:
a. dinoflagellate
b. choanoflagellate
c. euglenia
d. ameba
e. fungi
b. choanoflagellate
53
what is the primary role of a mushroom's underground mycelium:
a. absorbing nutrients
b. anchoring
c. sexual reproduction
d. asexual reproduction
e. protection
a. absorbing nutrients
54
which of the following statements is not true:
a. fungi are saprophytic
b. fungi are never photosynthetic
c. mycorrhizae help some plants grow
d. fungi are extracellular digesters
e. all fungi are multicellular
e. all fungi are multicellular
55
what does the contractile vacuole of an amoeba do:
a. controls the shape of the cell
b. controls the water content of the cell
c. help the cell move
d. helps the cell digest food
b. controls the water content of the cel
56
true or false: most viruses have a broad range of hosts
false
57
what are viruses made of:
a. some form of protein coat, and nucleic acid
b. always an envelope, capsid and DNA
c. only nucleic acid
d. always tegument and nucleic acid
a. some form of protein coat, and nucleic acid
58
EBV, the cause of mono, is a large, ds DNA virus surrounded by an envelope. according to the Baltimore scheme, its classified as:
a. group I
b. group II
c. Group III
d. group IV
e. Group V
a. group I
59
```
some E. coli divide themselves every min into 2 equal parts that are each he same size as the original organism. the Petri dish is which we started observing this process was full at 12.00.
when was it half full?
a. 6.00
b. 9.00
c. 11.30
d. 11.59
```
d. 11.59
60
you ingest 200 Salmonella enteric cells. They all make it through your stomach and into the intestine where they start to multiply. the average generation period is 2 hours. you eel sick when there's > 1.5 million present. how long will this take?
a. about an hour
b. about a day
c. about 3 days
d. about a week
e. about a month
b. about a day
61
bacterial cultures go through a lag because:
a. they gradually begin to die
b. they are synthesizing new enzymes in order to use nutrients in their medium
c. they are being exposed to increasing amounts of their own waste product
d. the DNA and protein synthesis in the culture has not caught up with cell division
b. they are synthesizing new enzymes in order to use nutrients in their medium
62
which of the following is not an example a microbial biofilm:
a. dental plaque
b. cryptogamic crust
c. pond scum
d. boat hull biofouling
b. cryptogamic crust
63
which method would you choose to get an overall picture of the bacterial species present in a given ecosystem?
a. metagenomics
b. proteomics
c. metabonomics
d. phylogenomics
e. metatranscriptomics
d. phylogenomics
64
what kind of organisms can grow within the aphasic zone?
a. phototrophs and lithotrophs
b. lithotrophs only
c. heterotrophs only
d. phototrophs, heterotrophs and lithotrophs
e. heterotrophs and lithotrophs
e. heterotrophs and lithotrophs
65
true or false: some bacteria can be seen with the naked eye
true - Thiomargarita namibiensis
66
what percent of known microbes can be cultured using traditional methods?
0.1%
67
what did Sergei Winogradsky do?
- among 1st to study bacteria in natural habitat
- discovered lithotrophs
- developed enrichment cultures
- built Winogradsky column
- showed importance of bacteria in geochemical cycling
68
what are endosymbionts?
organisms that live symbiotically inside other organisms
69
what did Lynn Margulis do?
Proposed that eukaryotic organelles, such as mitochondria and chloroplasts, evolved by endosymbiosis from prokaryotic cells engulfed by proto-eukaryotes
70
what did carl Woese discover?
prokaryotes in hot springs:
| Archaea
71
what are some stresses prokaryotes face
predation
nutrition limitation
osmotic stress
temperature/pH fluctuation
72
what traits do all prokaryotes share?
- thick, complex outer envelope
- compact genome
- tightly coordinated cell functions
73
what comes in a Mollicutes?
DNA
Ribosomes
Cytoplasm
Plasma membrane
74
pros of mollicutes
- doesn’t require a lot of energy to survive
| - Small -compact and can squeeze through small space
75
cons of mollicutes
- Difficult to maintain –usually needs a eukaryotic host cell to keep it safe
- Complicated diet required (cannot synthesize many of its required nutrients)
76
how many genes required for life have an unknown function?
149/473
77
what are cell walls made up of?
- Peptidoglycan
- Polymer of sugars and amino acids
- Sugars are N-acetyl glucosamine and N-acetyl muramic acid
78
what is a gram positive bacteria composed of?
```
DNA
Ribosomes
Cytoplasm
Plasma membrane
Thick cell wall (20-80nm)
```
79
pros of the gram positive model
- Strong –teichoic acid threads through the peptidoglycan layers, adding strength
- Resistant to osmotic lysis
- several pleasing shapes to choose from (coccoid, rod, spiral)
- Available in Gram stained purple!
80
cons of the gram positive model
- Must be kept away from lysozyme at all costs!
| - Sensitive to antibiotics that target the cell wall (e.g. penicillin)
81
what is a gram negative bacteria composed of?
- DNA
Ribosomes
Cytoplasm
Plasma membrane
Thin cell wall (just 1 or 2 sheets of peptidoglycan)
Outer membrane (contains lipopolysaccharide)
82
pros of gram negative model
- Able to defend itself against a wide range of toxic molecules
- Has a built-in storage compartment –the periplasmic space
- Resistant to osmotic lysis
- A wide range of pleasing shapes to choose from
- Available in Gram stained red
83
cons of gram negative model
- toxic if not handled correctly
- Requires a bigger genome to make the more complex cell wall
– can be expensive to maintain
84
examples of gram negative
E. coli
| h pylori
85
what is the waxy model?
mycobacterial cell envelope
86
describe the mycobacterial cell envelope
- Most complex of all bacterial cell envelopes
- Include unusual membrane lipids (mycolicacids)
- Form thick, waxy surface that is exceptionally hydrophobic and resistant to chemicals (and phagocytosis)
- Acid fast bacilli
87
what are mycobacteria resistant to?
```
Osmotic lysis
Detergents
Dryness
Many disinfectants
Most antibiotics
Oxidative bursts
Phagocytosis
```
88
what's the downside to mycobacteria?
often very slow growing
89
describe the S-layer
- S = ‘Surface’ (5-25nm thick)
- An additional protective layer (bacterial chainmail!)
- Crystalline layer of thick subunits
- Highly ordered
- Can flex to allow movement of molecules
90
what is the S-layer composed of?
Protein or glycoprotein
91
what is the capsule also known as?
the slime layer
92
why does the capsule appear as clear halos around the cell?
hard to stain
93
why is the capsule also known as the slime layer?
Consists of a slippery coat of loosely bound polysaccharides
94
what is the role of the capsule?
important role in pathogens
| for preventing phagocytosis/activation of the innate immune system
95
true or false: you can have a thylakoid in a gram positive option
false: only gram negative
96
what is the thylakoid made of?
- Specialist systems of extensively folded lamellae (sheets) of membranes
- packed with photosynthetic proteins and electron carriers
97
what does the thylakoid do?
Maximize photosynthetic capability of the cell
98
what organism is responsible for ~50% of atmospheric O2?
Prochlorococcus marinus
99
true. or false: carboxysomes are only available for gram negative?
true
100
describe carboxysomes
Contain enzymes used to fix CO2
- Found in all cyanobacteria as well as some chemotrophs that fix CO2
- Have a characteristic polyhedral shape
101
where are gas vesicles able to be present?
aquatic, photosynthetic variants
| some heterotrophs
102
describe gas vesicles
Thin ‘balloons’ made of extremely hydrophobic protein
| - Allow a microbe to maintain a set buoyancy optimal to its preferred conditions in the water column
103
what do storage granules do?
- store excess energy to be used when nutrients are low
104
how is energy stored in storage granules?
Usually stored in the form of glycogen, polyhydroxybutyrate (PHB) (biodegradable plastic) or poly-3-hydroxyalkanoate (PHA)
105
where can magnetosomes be present?
gram negative, aquatic species
106
what are magnetosomes and what do they do?
- Membrane-bound crystals of magnetite (Fe3O4)
| - Allow a motile bacterium to orient itself with the Earth’s magnetic field
107
what are advantages of magnetosomes?
narrow size distribution (25–55nm)
- uniform morphology
- high purity
- presence of a membrane (lipids and proteins)
108
pili can be:
- long or short
- flexible or brittle
- curly or straight
- singular or twisted together in rope-like bundle
109
what do pili do?
- important organelles for bacterial adhesion
- Some types are used in bacterial sex (conjugation)
- Some types are used in a specialist type of bacterial motility –‘twitching motility’
110
what do pathogens use pili for?
attach to host cells and initiate disease
111
what are stalks?
- Membrane-embedded extension of the cytoplasm of some aquatic bacteria
- Gram Negative option only
112
what do stalks do?
- Tip of stalk secretes factors –“Holdfasts”
- Act as an antenna to seek out nutrients (particularly phosphates)
- Allow bacterium to remain in a favourable location
113
what are rotary flagella?
- Organelles of motility
- Available for both G+ and G-models
- Rigid, long, helical, protein structures
- Anchored in the cell membrane (G+) or outer membrane (G-)
114
true or false: rotary flagella are anchored in the cell membrane for G-
false: that's from gram positive
| gram negative in the outer membrane
115
what do rotary flagella do?
work together with chemoreceptors to propel bacterium in optimal directions using ‘runs’ and ‘tumbles
116
how fast do flagellum turn?
1000 - 30,000rpm
117
what do nanotubes do?
- Especially important for biofilm-forming microbes
- Allow transmission of material between cells
- Can occur cross-species
118
what are nanotubes?
- Extensions of the cell envelope that connect the cytoplasm (or periplasmin G-bacteria) between 2 different cells
119
what is a thermophile?
archaea that likes the heat
120
describe Pyrococcus furiosus
a thermophile as well as a barophile
- Can only survive at temps >70C (prefers 100C!)
- An anaerobe that metabolizes sulfur to H2S
- Lives in deep-sea hydrothermal vent
121
what are psychrophiles?
Largely uncultured archaea: anaerobic heterotrophs, sulfate reducers or nitrite-reducing methanotrophs Live in deep, permanently cold water
122
what are halophiles and give an example
example: Haloquadratum walsbyi
- Likes hypersaline pools and in some extreme salt pools may be the only life form present
- Phototroph that forms fragile sheets that float near the surface of the water
- Uses gas-filled vesicles to float
123
what are acidophilus and give an example
example: Ferroplasma acidiphilum
- Oxidizes sulfur from FeS2 to form H2SO4
- Generates pH of 0 (or less!)
- Has no cell wall
- Can be found in acid mine tailings
124
what do methanogens do?
- able to generate methane from CO2and H2, formate, acetate and other small molecules
- Rely on bacterial species to provide them with essential nutrients
125
what is the basic reaction for methanogens
CO2+ 4H2--> CH4+ 2H2O
126
archaea cell membrane vs. bacterial
* Archaea use L-glycerol linked to side chains using ether links
* Bacteria use D-glycerol linked to side chains suing ester links
127
what do archaea have instead of fatty acid?
side chains composed of repeating units of isoprene
128
describe phototrophic archaea
- do not use chlorophyll and are not photosynthetic
•Instead use a retinal-based ion pump called ‘bacteriorhodopsin’
•Ion pump is coupled to ATP synthesis for the cell
129
what is more complex in eukaryotes than prokaryotes?
structure and form
130
what is more complex in prokaryotes than eukaryotes
metabolism
131
what did all eukaryotes descend from?
an ancestral cell that engulfed a bacterial endosymbiont–which became a mitochondrion
132
what did all phototrophs eukaryotes descend from?
an ancestral cell that additionallyengulfed the bacterial ancestor of chloroplast
133
how much of eukaryote DNA sequence is noncoding?
50-90%
134
what clade do animals and fungi fit into?
opisthokonts
135
what did the first choanoflagellate sequence reveal?
- Five immunoglobulin genes
•Yet choanoflagellates have no immune system
•Collagen, cadherin and integrin domains
•Yet choanoflagellates have no skeleton nor any matrix binding cells together
•Tyrosine kinase genes
•Yet choanoflagellates are not known to communicate/signal with each other
136
characteristics of fungi
```
- eukaryotes
•Reproduce using spores
•Unicellular forms
•Heterotrophic
•Absorptive nutrition
•Cell walls made of chitin
•Cell membranes contain ergosterol
•Nature’s recycler
```
137
describe yeast
```
- unicellular fungi
•Do not use hyphae to obtain nutrients
•Some yeasts are dimorphic
•Either unicellular or have mycelia, depending on the environmental conditions
•Important in food manufacture
```
138
life cycle of yeast
alternates between haploid (1n) and diploid (2n) forms
139
explain yeast haploid form
develops gametes for fertilization, producing a 2n zygote
140
explain yeast diploid form
undergoes meiosis, restoring the haploid form
141
how do fungi grow hyphae?
with cell walls of chitin
142
what is chitin
- Chitin consists of beta-linked polymers of N-acetyl glucosamine
•Has immense tensile strength (greater than that of steel!)
•Enables it to penetrate even tough food source
143
what is the mycelium?
A branched mass of extending hypha
144
describe characteristics of truffles
- Fruiting body of a subterranean mushroom
- Grow symbiotically with trees such as hazel and oak
•Weight for weight, more valuable than gold
•Requires a good truffle pig or dog to locate them
145
what are ophiocordyceps?
- Fungal spores enter ant’s body through enzymic action
| - Somehow interfere with brain activity, and make ant behave very strangely
146
what is fly agaric also known as
santa's little helper
147
describe fly agaric
- A 'true mushroom’
•In the same family as some of the most toxic mushrooms known
- less toxic but has hallucinogenic properties.
148
what are microsporidia?
fungi that have lost much of their genomes and have non-functional mitochondria
149
true or false: water molds have fungus like filaments that infect plants and a
true
150
describe Amebas
- Look like microscopic, amorphous lumps of jelly
•Have ‘ectoplasm’ and ‘endoplasm’
•Able to move through the production of pseudopods(false feet)
•Undertake highly controlled, complex motion
•Free-living predators in soil or water
151
how do amebas engulf their prey?
using phagocytosis
152
what is the brain eating amoeba?
Naegleria fowlerii
153
describe slime molds
- Used to be thought of as fungi (hence mold)
•have cellulose, not chitin, in their cell walls
•Single celled communities of ameba
154
what are radiolarians?
Amoebas with shells (tests) made of silica
155
what is algae?
* Primary producers in most ecosystems
| * Can be primary and secondary symbionts
156
describe primary endosymbiotic algae
- share their lineage with plants
•Useful models of plant physiology
•2 major clades
157
what are the 2 major clades of primary endosymbiotic algae
chlorophyta (green algae)
| rhodophyta (red algae)
158
what are the 2 secondary endosymbiotic algae?
diatoms
| kelps
159
describe diatoms
-Unicellular algae with a unique, protective bipartate shell made of silica (glass)
•Frustules
•Dead diatoms sink to the sediment and form ‘diatomaceous earth
160
describe kelp
- brown algae’
•Store lipids such as leucocin for energy needs
•Unrooted, they form floating forests that support diverse ecosystems
161
what are alveolate?
- Named for the flattened vacuoles (alveoli) within their outer cortex
•Most have cilia or flagella
•Highly structured)
•Are generally predators
•Complex genetic system, sexual reproduction
162
what are dinoflagellates
phototrophic alveolates
| possess 2 flagella
163
what is the James Bond protist and why is it called this?1
Euplotidium
| its called this because it causes bacteria to extrude their cell contents
164
what do apicomplexans use to gain entry to host cells?
an apical complex
165
definition of virus
a non-cellular particle that must infecta hostcell, where it reproduces
166
true or false: viruses can infect everything except other viruses
false: they can infect viruses too
167
what is host range?
each species of virus infects a particular group of host species
168
what are the different types of virus structures?
```
icosahedral
filamentous
multiple helical packages
complex viruses
asymmetrical viruses
```
169
characteristics of icosahedral virus structure
- 20 triangular faces –the largest number possible
| - Natural selection has favoured the packaging of the most material within the smallest number of repeating sub units
170
characteristics of filamentous virus structure
- Genome (in this case RNA) is coiled into the helical capsidstructure
- Can vary in size to accommodate varying lengths of genomic material
171
characteristics of multiple helical packages virus structure
- enables influenza virus to package different numbers of RNA segments into different virions
- Process enables rapid evolution of new strains
172
characteristic of complex viruses structure
Icosahedral head coat plus a helical ‘neck’ that acts as an elaborate delivery device
173
characteristics of asymmetrical viruses structure
* No symmetrical capsid: the double-stranded DNA genome is stabilized by covalent connection of its 2 strands at each end
* Instead of a capsid, the DNA is enclosed by a core envelope surrounded by an outer membrane
* Contain a large number of accessory proteins
* Appear to have evolved from degenerate cell
174
describe viral genomes
Usually very simple, and genes are efficiently packaged
175
what are viroids?
- extremely simple viruses: there is no protective capsid
•Usually RNA molecules that infect plants
•Some have catalytic activity
176
what do prions consist of
protein only
177
how do prions work?
- interaction with the normal form of the protein results in transformation to the prion form
- Multiple prion proteins aggregate and cause cell death, creating sponge-like holes in brain tissue
178
how are viruses classified?
•Genome composition
•Capsid symmetry
•Envelope (presence or absence, and structure, if present)
•Size of virus particle (range from 30-400nm across;
•Host range (not always very useful
- promotes
179
what is the most important criterion in classifying viruses?
genome composition
180
7 ways mRNA is produces by a virus
| Baltimore classification
```
Group I: dsDNA viruses
Group II: ssDNA viruses
Group III: dsRNA viruses
Group IV: (+)sense ssRNA viruses
Group V: (-) sense ssRNA viruses
Group VI: retroviruses
Group VII: pararetroviruses
```
181
what is Group I: dsDNA viruses
- make their own DNA polymerase (or use the host’s)
| •Transcribe their genes using a standard RNA polymerase (or use the host’s
182
what does Group I: dsDNA viruses consist of?
bacteriophageT4, Giruses, baculovirus, pox viruses, and most known archaeal viruses
183
what is Group II: ssDNA viruses
- require host DNA polymerase to generate the complementary strand
•(resulting dsDNA can then be transcribed by the host RNA polymerase)
184
what does Group II: ssDNA viruses consist of?
bacteriophageM13, parvovirus, geminivirus
185
what is Group III: dsRNA viruses
- require a viral RNA-dependent RNA polymerase to generate mRNA
•Because this RNA polymerase is required immediately after infection, it’s usually made and packaged in the virion
186
what does Group III: dsRNA viruses consist of?
reovirusessuch as rotavirus and phytoreovirus
187
what is Group IV: (+)sense ssRNA viruses
(+) strand is the coding strand
•Serves directly as mRNA
• needs synthesis of the (-) strand to make a ds intermediate for replication purposes
188
what does Group IV: (+)sense ssRNA viruses consist of?
poliovirus, rhinovirus, rubella virus, coronaviruses(e.g. SARS), flaviviruses(e.g. West Nile virus)
189
what is Group V: (-) sense ssRNA viruses
- Genomes consist of template RNA
•Require a viral RNA-dependent RNA polymerase for transcription of (-)RNA to (+)mRNA
•May be segmented viruses (and thus can recombine and evolve quickly
190
what does Group V: (-) sense ssRNA viruses consist of?
s influenza virus, hantavirus, ebolavirus, rabies virus, measles virus
191
what is Group VI: retroviruses
(+) strand RNA genomes, RNA reverse transcribing viruses
•Instead of RNA polymerase they package their own reverse transcriptase
•Transcribes the RNA into dsDNA
•dsDNA gets incorporated into the host genome and directs the expression of the viral gene
192
what does Group VI: retroviruses consist of?
HIV, SIV, FL
193
what is Group VII: pararetroviruses
DNA reverse transcribing viruses
•require reverse transcriptase (viral or host
)•Copy genomes into RNA
•Then reverse transcribe this to DNA
194
what does Group VII: pararetroviruses consist of?
hepatitis B virus, cauliflower mosaic virus
195
what is HERV?
•Human Endogenous Retroviruses
•Make up 8% of the human genome
- remains of ancient viruses that once infected the germline and incorporated themselves into our genome
•Over the millennia, they have become degraded and non-functional
196
Edward Jenner vaccinated against smallpox using:
a) Killed smallpox virus
b) A recombinant protein derived from smallpox
c) Live cowpox virus
d) Killed cowpox virus
e) A toxoid
c) Live cowpox virus
197
lithotrophs are:
a) Organisms that use light to obtain energy
b) Organisms that prefer to live under high pressure
c) Organisms that use minerals for biosynthesis
d) Usually protists
e) Always able to survive at high temperature
c) Organisms that use minerals for biosynthesis
198
Treating cows with antibiotics against cellulolytic bacteria:
a) Would prevent shedding of pathogens such as Escherichia coli 0157:H7 by the cows
b) Would permit the cows to obtain sufficient nutrition from plant materials
c) Would have an overall beneficial effect on the microbiota
d) Would inhibit the ability of the cow to obtain sufficient nutrition from foods such as hay
e) Would improve the health of the animal
d) Would inhibit the ability of the cow to obtain sufficient nutrition from foods such as hay
199
Carl Woese pioneered:
a) The use of mitochondria in endosymbiotic theory
b) A method to sequence DNA
c) The use of Gram staining in identifying bacteria
d) The study of molecular biology
e) The use of rRNA to build phylogenetic tree
e) The use of rRNA to build phylogenetic tree
200
Bacteriorhodopsin is:
a) A retinal-containing transmembrane protein
b) A retinal-containing cytoplasmic protein
c) A chlorophyll-containing cytoplasmic protein
d) A chlorophyll-containing transmembrane protein
e) Only found in bacteria
a) A retinal-containing transmembrane protein
201
Fungi:
a) Benefit animals and plants
b) Mainly harm plants and benefit animals
c) Mainly harm animals and benefit plants
d) Neither benefit nor harm animals or plants
e) Can both benefit and harm animals and plants
e) Can both benefit and harm animals and plants
202
The Protozoa are _________________________ and usually ________________:
a) Prokaryotes / Unicellular
b) Eukaryotes / Unicellular
c) Eukaryotes / Amitochondriate
d) Eukaryotes / Multicellular
e) Parasitic / Saprophytes
b) Eukaryotes / Unicellular
203
. Organisms A, B and C are all found in one community. Organism A utilizes glucose andgenerates lactate. Organism B converts lactate to CO2 + Hydrogen, and organism C generatesmethane from the hydrogen and CO. This relationship between organisms A, B and C is called:
a) Metabolism
b) Commensalism
c) Syntropism
d) Competition
e) Ecosystem
c) Syntropism
204
Viroids are:
a) Small stretches of RNA encased in a primitive capsid
b) Small stretches of DNA encased in a primitive capsid
c) Infectious particles that usually infect archaea
d) ‘Naked’ infectious RNA molecules
e) ‘Naked’ infectious DNA molecules
d) ‘Naked’ infectious RNA molecules
205
Prokaryotes called ___________ do not have a cell wall, and the ___________ do not have peptidoglycan.
a) Archaea / Mycobacteria
b) Mycoplasma / Archaea
c) Mycobacteria / Gram-negative bacteria
d) Streptococcus / Pseudomonas aeruginosa
e) Plasmodium / slime molds
b) Mycoplasma / Archaea
206
in a lichen, the ____________ provides protection, and the Cyanobacterium provides ___________:
a) algae / vitamins
b) fungus / sunlight
c) Rhizobium / nitrogen compound
d) fungus / organic molecules
e) algae / organic molecules
d) fungus / organic molecules
207
Acid fast bacteria can be stained in the Ziehl-Neelsen procedure using:
a) carbolfuschin
b) saffranin
c) India ink
d) phenol red
e) crystal violet
a) carbolfuschin
208
if you had a cell with the structures listed below, what would be the outermost layer of this hypothetical cell?
a) Outer membrane
b) Capsule
c) Surface (S)-layer
d) LPS
e) Arabinogalactan
b) Capsule
209
which terms describe a prokaryote that grows best at 100°C at pH 2 and has specific requirement for light and carbon dioxide?
a) Photoautotrophic, acidophilic, hyperthermophile
b) Photoautotrophic, acidophilic, thermophile
c) Hyperthermophilic, barophilic, chemolithotroph
d) Thermophilic, alkaliphilic, autotroph
e) Hyperthemophilic, alkaliphilic, phototroph
a) Photoautotrophic, acidophilic
210
Which terms describe a prokaryote that grows best at 25°C at pH 10 and has a specific requirement for organic carbon for growth?
a) Psychrophilic, heterotrophic, alkaliphilic
b) Mesophilic, chemolithotrophic, alkaliphilic
c) Photosynthetic, psychrophilic, heterotrophic
d) Mesophilic, heterotrophic, alkaliphilic
e) Thermophilic, autotrophic, alkaliphilic
d) Mesophilic, heterotrophic, alkaliphilic
211
Thylakoids are:
a) Sites of photosynthesis in chloroplasts and cyanobacteria
b) Storage granules specifically found inside photoautotrophs
c) Membranes of mitochondria
d) Often associated with the nucleoids of bacteria
e) Ancient precursors of chloroplasts
a) Sites of photosynthesis in chloroplasts and cyanobacteria
212
Teichoic acids are:
a) Found in Gram negative cells only
b) Found in Gram positive cells only
c) Are a form of bacterial lipid
d) A cytoplasmic molecule
e) A stabilization factor for the bacterial nucleoid
b) Found in Gram positive cells only
213
.A bacterial cell with a tuft of flagella emerging from one pole only is said to be:
a) Monotrichous'
b) Piliated
c) Peritrichous
d) Non-motile
e) Lophotrichous
e) Lophotrichous
214
Bacterial flagella are usually:
a) Long, helical, flexible
b) Powered by ATP
c) Short, helical, inflexible
d) Powered by a proton motive force
e) Made of microtubule
d) Powered by a proton motive force
215
Nitrogen fixing bacteria:
a) Are always associated with legumes encased in their root nodules
b) Convert nitrate to nitrogen gas
c) Contribute to atmospheric pollution
d) Convert nitrogen gas to ammonia
e) Are always anaerobic
d) Convert nitrogen gas to ammonia
216
Animals are most closely related to:
a) Choanoflagellates
b) Amoeba
c) Green algae
d) Fungi
e) Diatoms
a) Choanoflagellates
217
Protists are:
a) Always unicellular
b) A paraphyletic group of organisms
c) Usually photosynthetic
d) A group that excludes protozoa
e) Only able to reproduce asexual
b) A paraphyletic group of organisms
218
The node of a phylogenetic tree:
a) Demonstrates early divergence from an ancestral cell
b) Demonstrates recent divergence from an ancestral cell
c) Is always drawn as a vertical line
d) Is the root, indicating the most distantly related species
e) Represents the last common ancestor of the associated branches, which no longer exist
e) Represents the last common ancestor of the associated branches, which no longer exist
219
A girus is a giant virus that:
a) Has a peptidoglycan cell wall
b) Is able to replicate outside of a host cell
c) Has an unusually large genome
d) Is known to infect metazoans
e) All of the above
c) Has an unusually large genome
220
The bacterial slime layer, or capsule, is:
a) A slippery outer layer of loosely bound polysaccharides
b) Also known as S-layer
c) Made of murein
d) Easily stained with crystal violet
e) Used by the bacterium to prevent dessication
a) A slippery outer layer of loosely bound polysaccharides
221
The part of a bacterial cell that is being investigated for use as a biodegradable plastic is:
a) Plasma membrane
b) Storage granule
c) Magnetosome
d) Carboxysome
e) Teichoic acid
b) Storage granule
222
Group IV viruses in the Baltimore classification system are viruses that are:
a) Single stranded, positive sense RNA viruses
b) Retroviruses
c) Double stranded DNA viruses
d) Single stranded, negative sense RNA viruses
e) Single stranded DNA viruses
a) Single stranded, positive sense RNA viruses
223
Which of the following is not a DNA virus?
a) parvovirus
b) bacteriophage M13
c) rhinovirus
d) Smallpox virus
e) bacteriophage T4
c) rhinovirus
224
Burst size is:
a) The number of bacterial cells lysed by a virulent phage
b) The number of viral particles released by a phage during the lytic phase
c) The capacity of a bacterial cell cytoplasm for hosting assembled bacteriophage
d) The number of bacterial cells required in order to visualize a plaque
e) Always higher for archaea than bacteria
b) The number of viral particles released by a phage during the lytic phase
225
Which of the following statements is false about mycorrhizae?
a) Mycorrhizae are essential to all plant life
b) Mycorrhizae help plants to assimilate extra nutrients from the soil
c) In return for mycorrhizae activity, plants reward the associated fungus with nutrients such as sugars
d) The mycorrhizae from a single fungus can stretch underground for several kilometers
e) Mycorrhizae aid in nutrient assimilation from soil because they offer a much larger surface area for absorption than plant roots.
a) Mycorrhizae are essential to all plant life
226
how do humans protect against microbial invaders?
- Non-specific defences
| •Adaptive and non-adaptive immune defences
227
what percentage of your weight is compromises microbes on/in your body?
a. 0.05-0.09
b. 0.1-0.9
c. 1-3
d. 4-5
e. 6-10
c. 1-3
228
what are pathobiots?
life in/on us but don't do use any harm until we get sick, then they take advantage of us
229
what are commensal
| organisms?
Bacteria normally found at various non-sterile body site
230
what is the Microbiota?
- The consortium of colonizing microbes
| - indicates the cell consortium
231
what is the microbiome
- The consortium of colonizing microbes
| - indicates the genetic potential of the consortium
232
what do ruminants rely on microbes for?
digestion of cellulose
233
why do some insects require microbes
allow digestion of their dietary substrates
234
true or false: microbes can cause a disease if they reach an abnormal location
true
235
how many bacterial species are there per individual?
~200
236
true or false: there's more human genes than microbial genes associated with us
false: at least 100x more microbial genes associated with us than our human gene
237
what microbes lives on our face
demodex mites
238
ratio of bacteria to human in humans
1.3 bacteria to 1 human
239
which these diseases is thought to emerge as a result of an imbalanced microbiota
a) autism
b) colorectal cancer
c) type 1 diabetes
d) chronic depression
e) Parkinson's disease
all of them!
240
why is the skin difficult for microbes to colonize
Dry, salty, acidic, protective oils
241
where are most microbes on the skin and how many are there?
moist areas:
Scalp, ears, armpits, genital and anal area
10^12
242
what kind of bacteria colonize the skin?
gram positive
243
what is body odour the result of?
microbes breaking down certain things causing the bad smell
244
what is a human infants mouth colonized by?
Non-pathogenic Neisseriaspp. (Gram negative cocci)
| •Streptococcus, Lactobacillus spp. (Gram positive rods
245
as teeth emerge, what other bacteria begin growing in the mouth
Prevotella and Fusobacteriumspp.: between gums and teeth •Streptococcus mutans: tooth enamel
246
what is the most common site of infection in humans?
oral and respiratory tract
247
what are nostrils and nasopharynx dominated by?
Firmicutes and Actinomycetes
248
what is nasopharynx populated by?
Staphylococcus aureus and S. epidermidis
249
what is oropharynx composition similar to?
microbes to saliva
250
what kind of microbes mainly live in the lungs
anaerobes
251
where in the body are usually sterile or near sterile?
kidney and urinary bladder
252
what are virulent bacteriophages?
Bacteriophages which predominantly carry out the lytic pathway
253
what are temperate bacteriophages?
Bacteriophages which predominantly carry out the lysogenic pathway
254
what is a prophage?
the bacteriophage DNA as part of the host genome
255
what kind of immune system do bacteria and archaea have?
an adaptive immune system
256
how do prokaryotes multiple?
through binary fission
257
what is most prokaryote genomes made of?
DNA that is formed into a loop
258
describe bacterial DNA replication
- semi-conservative
| - bidirectional
259
what is vertical transmission
binary fission
260
define binary fission
identical genome copies produced
261
what is horizontal transmission?
- transformation
- transduction
- conjugation
262
what is bacterial transformation?
- uptake of naked DNA by a bacterium to use in its own genome
- uptake of plasmid DNA by a bacterium for continued autonomous replication of the plasmid in a new host
263
what is a plasmid
extra chromosomal DNA, usually much smaller than the chromosome itself
•Usually encode accessory function
264
how do plasmids replicate?
Replication is autonomous
| •i.e. not tied to the replication of the chromosome
265
what does conjugation require?
- cell-cell contact that is mediated by a structure called the ‘sex pilus
- presence of F+
266
true of false: packaging viral DNA into capsids is a sloppy process
true
267
what is the bacterial species with the fastest generation time?
Clostridium perfringens
| 10 mins
268
what is the bacterial species with the lowest know generation time?
Mycobacterium leprae
| 14 days
269
what are the 4 phases of bacterial growth?
lag phase
exponential phase
stationary phase
death phase
270
describe early exponential phase of bacterial growth
cells growing at the maximum rate possible based on conditions available
271
explain late exponential phase of bacterial growth
slowing of growth rate due to cell density
272
why do cell numbers stop rising in the stationary phase of bacterial growth?
- Lack of a key nutrient
| •Build up of waste product
273
what do cells do to survive during the stationary phase of bacterial growth?
- Become smaller
•Produce stress response proteins
•Some may sporulate
274
what do chemostats do?
allow growth phase to be controlled
275
what is bacterial cell sporulation?
- Certain G+ genera are able to place themselves into suspended animation when the going gets tough
•Endospore formation
•An alternative pathway in the growth cycle
276
true or false: endospores tend to be very weak
false: very strong
277
what happens to cells that can't sporulate?
```
- Cells get smaller
•Cell walls get thicker
•Glycogen stores are laid down
•Nutrient transporters are expressed
•Stress response proteins are expressed
```
278
what are fimbrial jackets?
elaborate coats that some bacterial species knit themselves made out of cellulose and fimbrial proteins
279
how can biofilms be bad?
can damage equipment,
can contaminate abiotic surfaces introduced in the body,
can cause tooth decay
280
how can biofilms be good?
allow microbes to work together to effectively metabolize
281
what are biofilms?
a thin, slimy film of bacteria that adheres to a surface
282
true or false: biofilms are composed of only one bacterial specie
false: Biofilms may be composed of a single bacterial species or of several collaborating species
283
what binds biofilms together?
Exopolysaccharides
284
what are oligotrophs?
bacteria in most soil and water ecosystem
285
describe oligotrophs
- Have a high rate of growth at low nutrient concentrations•
Will die if given rich media sources
•Many aquatic bacteria once considered to be ‘unculturable’ can actually be easily cultured in low nutrient concentration
286
what is an ecosystem?
collection of populations of species + their habitat
287
what is a population?
a group of species living in a common location
288
what is a community?
The sum of all the populations of different species
289
what is a niche?
a set of conditions enabling an organism to grow and reproduce
290
true or false: every molecule in nature can be used as a source of carbon or energy by a microorganism somewhere
true
291
true or false: Microbes are found in every environment on Earth
true
292
describe phylogenomics
Profiling ecosystem composition based on taxonomic reference genes such as the 16S rRNA gene
293
describe metagenomics
•Sequencing and assembling entire genomes from ecosystem
294
describe Metatranscriptomics (meta-RNAseq)
•Sequencing entire collections of mRNA from an ecosystem and mapping the reads back to genomes to identify them
295
describe proteomics
Obtaining amino acid sequences and identifying the collection of signatures from a given ecosystem
296
describe lipidomics
Using advanced chromatography and spectroscopy techniques to identify lipid signatures in a given ecosystem
297
describe metabolomics
Using various analytical chemistry methods to detect and identify molecules from an ecosystem
298
how do microbes contribute to an ecosystem?
Utilize their collectively diverse metabolisms to acquire energy and assimilate elements into biomass
•Detoxify wastes
•Protect symbiotic partners from predation and/or hostile environments
• modulate a host’s development and behaviour
299
what is assimilation?
processes by which organisms acquire an element to build into cells
300
what are primary producers?
Organisms that produce biomass from inorganic carbon
301
true or false: if the organic compound is not in the environment, microbes can assimilate it from mineral (inorganic) sources
true
302
what is dissimilation?
The process of breaking down organic nutrients into inorganic minerals (usually through oxidation)
303
what are the most common assimilatory and dissimilatory cycles known to biology?
carbon and nitrogen cycles
304
what does the food web rely on primary producers for?
- Absorbing energy from outside of the ecosystem
| •Assimilating minerals into biomass
305
what factors most influence the ecosystem?
```
availability to water
temperature
pH
salinity
availability to oxygen (or other electron acceptors)
```
306
what is symbiosis?
organisms adapting to the presence of other organisms
307
what is mutualism?
interactions between organisms of two different species, in which each organism benefits from the interaction in some way
308
what is synergism?
The interaction of things resulting in the overall effect that is greater than the sum of individual effects of any of them
309
what is commensalism?
members of one species gain benefits while those of the other species neither benefit nor are harmed
310
what is amensalism?
any relationship between organisms of different species in which one organism is inhibited or destroyed while the other organism remains unaffected
311
what is parasitism?
benefits at the expense of another organism usually of different species
312
what are the primary producers in the ocean?
bacteria and algae
313
what are 4 types of plankton?
1) Microplankton(20-200μm)
2) Nanoplankton(2-20μm)
3) Picoplankton(0.3-2μm)
4) Femtoplankton(<0.3μm)
314
where are radiolarians concentrated?
on top of contours of Chlorophyll A in the water
315
true or false: plankton tend to be found concentrated in thin layers
true
316
true or false: the stomach has a very low pH
true:
| fes microbes survive
317
which microbe survives in the stomach?
helicobacter pylori
318
what is decreased stomach acidity known as?
hypochlorydia
319
where is the most important microbial ecosystem in the human body?
the colon
320
what do you have in a gut microbial with a high diversity of species?
- healthy ecosystem
- balance
- functional redundancy
- resistance to damage
321
what do you have in a gut microbial with a low diversity of species?
- sick ecosystem
- imbalance
- functional disability
- susceptibility to damage
322
what are microbes called that break barriers when the host is compromised?
opportunistic pathogens or pathobionts
323
how is the microbiota protective?
competitive exclusion
environmental modification
host stimulation
324
what is a gnotobiotic animal?
An animal where the associated microbiota is knownand defined
325
what abnormal physiology do gnotobiotic animals have?
- poorly developed immune systems
- lower cardiac output
- require more calories
- thin, poorly developed intestinal walls
- abnormal ceca
- odd behaviour
- misshapen mitochondria
326
who is David Vetter?
- born with very impaired immune system
| - lived for 12 years in a completely sterile environment
327
where is the home of endoliths?
extreme cold: polar regions
328
wha makes archaea viruses different than bacteriophage ?
capsule is spindle-shaped with strange turrets
MICR 2420
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