Exam 2 Flashcards
(217 cards)
1
Q
Microbes can be categorized by…
A
- how they generate ATP - aerobic vs anaerobic
- where they get their carbon source
2
Q
autotrophs
A
- carbon from CO2 in air
- self feeders
3
Q
heterotrophs
A
- carbon from organic compound in their medium or diet
- different feeders
4
Q
most bacteria and animals are which: heterotroph, autotroph, chemotroph, phototroph
A
heterotroph
5
Q
chemotrophs
A
generate APT with chemical reaction
6
Q
phototroph
A
generate ATP with light energy
7
Q
phases of microbial growth
A
- lag
- log
- stationary
- death
8
Q
lag phase
A
- no growth
- cell recognizes nutrients available and gears up to use them
9
Q
log phase
A
- exponential growth when in favorable environment
10
Q
generation time
A
the time it takes a bacterial cell to divide - 10 minutes to 24 hours
11
Q
generation time of most disease-causing organisms
A
20-30 minutes
12
Q
What do you need to know to determine how long it will take for a pathogen to reach dangerous levels
A
- how quickly they can divide
- how many generations they have been able to accomplish
13
Q
calculate number of cells
A
initial number of cells x 2^number of generations
14
Q
stationary phase
A
- when the culture stops growing
- they have used up all nutrients and excreted lots of waste into the environment making it unfavorable
15
Q
death phase
A
- occurs 1-2 days after stationary phase as cells begin dying
- used up all ATP and have no way of producing more
16
Q
common requirements for growth
A
environment
nutrition
17
Q
nutritition is
A
any chemical from the environment used to build molecules needed to build new cells
18
Q
organic compounds require
A
carbon nitrogen oxygen sulfur phosphorus trace elements vitamins
19
Q
t/f - cells typically get their carbon and oxygen from the same place
A
true
20
Q
biproducts of oxygen that can be toxisc to the cell
A
hydrogen peroxide
superoxide
21
Q
dealing with H2O2
A
catalase converts it to water and oxygen so that it is not reactive
22
Q
another name for superoxide
A
free radical
23
Q
what is a superoxide
A
highly reactive oxygen with an unpaired electron that can kill the cell
24
Q
dealing with superoxide
A
superoxide dismutase converts the free radical to H2O2 which must then be converted by catalase to H2O and O2
25
t/f - oxygen can be toxic even to aerobic cells
true - its biproducts can be if not appropriately dealt with
26
ex of obligate aerobe
pseudomonas aeruginosa
eye infections
burn infection
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microaerophile
tolerate less oxygen than obligate aerobe and require more CO2
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ex of microaerophile
H.pylori
| stomach ulcers
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ex of facultative anaerobe
e.coli
30
aerotolerant anaerobe
generate energy without oxygen but are not killed by exposureto it
31
ex of aerotolerant anaerobe
streptococcus pneumoniae
32
ex of obligate anaerobe
clostridium
33
needed for cofactors and coenzymes
trace elements
34
trace elements include
potassium
copper
zinc
iron
35
vitamins are
organic growth factors
needed in small amounts
precursors of enzyme cofactors
36
thermophiles
* Like high heat – 50C+
* Can withstand boiling for several hours
* Colors around the silver springs are from thermophiles that different pigments
37
mesophiles
* Like moderate temp – 15-45C
* Survive in fridge
* Our body temp is their optimal
38
which concern us most: thermophile, mesophile, psychophile
mesophile
39
psychrophile
* Love cold
| * Grow best in the fridge and survive the freezer
40
most common pH range of microbes
5-8
41
halophiles
* like high salt concentrations
| * find in great Salt Lake and oceans
42
methods to measure growth
turbidity
direct count
plate count
most probable number (MPN)
43
turbidity
spectrophotometer calculates number of cells in a liquid culture
44
direct count
count individual cells by placing small amount of liquid culture in microscope slide called counting chamber
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plate count
put specific amount of liquid culture on agar plate, allow to grow colonies, count number of colonies
count living cells in a culture
46
most probable number
MPN
allows counting of living cells in liquid culture
47
what is used in water treatment plants to measure growth
most probable number
48
producer
produce products that are useful to other organisms
49
consumer
microbes that consume waste products we make
50
decomposer
microbes responsible for decomposing dead organic matter
51
carbon cycle
o CO2 in the atmosphere undergoes conversion to carbon that is used in most organic molecules for organisms on the planet
o Some bacteria fix carbon from CO2 so that it can be used by other organisms to make their components of their cells
52
methanogens
take carbon from organic material and covert it to methane
part of the carbon cycle
53
methane produced in the carbon cycle can be
used by some microbes as energy
used by humans as fuel ot create heat
54
nitrogen cycle
o Some bacteria fix nitrogen from the atmosphere to be used by other organisms to make biologically important molecules like proteins and nucleic acids
some bacteria convert nitrogen in the soil and decaying matter to gas
55
example of a nitrogen fixing bacteria from the atmosphere
clostridium
56
example of denitrifying bacteria
pseudomonas
| bacillus
57
pseudomonas
cause ear, eye, and burn infections
58
biofilms
microbial community
seen on surfaces of soil, rocks, boat docks, ac units
a way pathogens cause disease in our bodies
59
these microbes provide more than half of the oxygen for the planet
those living in marine environments
60
biochemical oxygen demand
BOD
| measure amount of organic matter in sewage by measuring the amount of oxygen needed by the microbes to metabolize it
61
steps of sewage treatment
primary treatment
secondary treatment
tertiary treatment
62
primary treatment of sewage
screens the sewage to remove the organic matter from the liquid. The organic matter settles into sludge
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secondary treatment of sewage
uses microbes to decompose organic matter
• Many microbes are aerobic, but there are some that are anaerobic
• Anaerobic deal with the solid sludge left from the primary treatment
64
tertiary treatment of sewage
involves additional filtering and chemicals to remove remaining microbes, phosphates, and nitrogen from the water
65
what is pollution
anything that makes water non-potable
| not clean
66
eutrophication
• Causes an overgrowth of algae that in turn causes an overgrowth of aerobic bacteria – as they grow they use up the O2 in the water leading to the death of the fish in the water
o Leads to a domino effect where the organisms relying on the fish will also die
67
sources of pollution
pesticides
petroleum products
plastics
68
bioremdiation
uses microbes to clean up pollution
69
ex of bioremediation
Pseduomnas to eat oil accidently spilled in the ocean
o Important to the nitrogen cycle but cause infection to humans
o Oil consumption by the bacteria is slow
70
bioaugmentation
o trying to increase the numbers of available microbes needed for bioremediation
o If we can grow a massive number of these needed microbes, we can place them on the polluted area to shorten the time needed to decompose the pollutant
71
genetics
the study of heredity and variation among organisms
72
DNA...
o Carries the genetic info needed to make a new cell
o Is a macromolecule
o Is made of the nucleotide guanine, cytosine, adenine, thymine
o Double stranded helix
o Found in chromosomes
73
gene
specific segments of DNA that contain the info needed to manufacture proteins and other macromolecules
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types of DNA reactions
replication
| gene expression
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when does DNA reproduce
when ready to produce a new cell
76
what enzyme is used for replication
DNA polymerase
77
DNA to DNA
replication
78
gene expression
information is dictated to the cell for proteins to be made
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steps for gene expression
transcription
| translation
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DNA to RNA
transcription
81
enzyme for transcription
RNA polymerase
82
RNA to protein
translation
83
ribosome is needed for
translation
84
why is transcription needed
DNA must be converted to RNA for the information to be produced by the cell
85
what is produced in transcription
mRNA complimentary to the strand used
86
describe transcription
1. RNA polymerase binds to promoter
2. DNA unwinds
3. RNA polymerase builds the mRNA
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describe translation
The mRNA made in transcription attaches to the ribosome which translates the message to build a protein molecule
88
a ribosome is like...
a factory
89
prokaryotic genome
one circular, dna chromosome
90
eukaryotic genome
many strands of dna chromosomes
91
chromosome
carries the genes essential for growth and reproduction of the cell
92
plasmids are
- Additional circular chromosome often found in bacteria
- Can replicate on their own
- Can carry genes that are not essential for growth and reproduction of the cell but give the cell an advantage of survival in special environments
93
examples of genes found on plasmids
* Pigment
* Certain pili for mating
* Toxin resistance
* Antibiotic resistance
94
who discovered plasmids
Pasteur
95
How were plasmids discovered
Pasteur was working with anthrax
• Grew anthrax in meat broth and heated it, but not enough to kill the bacteria, just enough to stress them
• Injected the heated bacteria into the animal
• The animal did not die
96
What did it mean that the animal did not die when injected with the heat treated anthrax
– the chromosome was intact but what ever allowed the bacteria to survive in our body and kill us was not there – it was on a plasmid that was ejected form the cell
97
Pasteur's observations with anthrax
o Difference in genetic makeup of the cells in the heated/not heated flasks
o The small circular dna was not necessary for growth and reproduction of the cell as they continued to grow and replicated even under heat
o The small circular dna seemed to help them survive certain environments
98
genetic variation in eukaryotes
- mutation
| - sexual reproduction
99
genetic variation in prokaryotes
- genetic transfer
| - mutation
100
mutation
any change in the chemical makeup of the cell's genotype
101
types of mutation
* Base substitution
* Deletion
* Inversion
* Transposition
* Duplication
102
how can mutations occur
spontaneously or induced by chemical, physical, biological treatments
103
ex of physical causes of mutation
uv light
| radiation
104
ex of biological causes of mutation
transposition
| jumping genes that move from one place to another
105
codon
3 bases read by a ribosome at a time
106
what gives a protein a specific shape and function
the arrangement of amino acids
107
base substitution
• Single nitrogen base is substituted for another
108
base deletion
• Single nitrogen base is deleted
109
inversion
• A set of bases reverses order
110
duplication
• A set of bases duplicates itself and sets the copy down next to the original set
111
transposition
• A set of bases moves from one place to another in the genome
112
Original: TheFatCatRanOff
Mutation: TheFrtCalRanOff
base substitution
113
Original: TheFatCatRanOff
Mutation: TheFtcAtrAnoFf
base deletion
114
Original: TheFatCatRanOff
Mutation: TheTafRanOff
inversion
115
Original: TheFatCatRanOff
Mutation: TheFatCatCatRanOff
duplication
116
Original: TheFatCatRanOff
Mutation: TheFatOffCatRan
transposition
117
forms of genetic transfer
conjugation
transformation
transduction
118
genetic transfer allows
bacteria to alter their genome and use this to their advantage
119
t/f - genetic transfer is essential to the life cycle of prokaryotes
false
120
transformation
Dna leaves one cell, exists in the extra-cellular environment, before it is taken into another cell
121
How was transformation discovered
Griffith and s.pneumoniae – smooth infectious cells died releasing their dna, this was taken up by rough not infectious cells which then became infectious
122
conjugation
Carried out by special plasmids
• The genes on the plasmid make a pilus between two cells
• The plasmid replicates itself and transfers the copy to the cell without the plasmid
123
allow cells to share traits like antibiotic resistance
conjugation
124
will conjugation occur if the recipient cell already has the desired plasmid
no
125
transduction
A virus infects a bacteria and reproduces, accidentally taking some bacterial DNA as its own. The virus, now with a piece of bacterial dna leaves the bacteria and moves to a new cell. The virus infects a second cell and injects the bacterial dna from the first cell into the genome of the 2nd cell
126
genetic transfer that occurs when a virus infects bacteria
transduction
127
allows us to recombine dna in the lab and enhance lives
biotechnology
128
another name for biotechnology is
recombinant dna technology
129
describe broadly the technique of biotechnology
o Collection of different procedures that takes dna from cell, manipulates the dna in a test tube, and then places in another cell – usually in a cell of a different species
130
a basic tool of biotechnology
gene cloning
131
gene cloning is
a way to obtain identical copies of a gene
132
steps of gene cloning
Find desired gene located in a cell and place into a vector, usually a plasmid
Put the recombined DNA into an appropriate host
Verify we have succeeded by using gel electrophoresis
Propagate the cells
• Cell mass will produce identical copies of the human gene as well as the gene produce
133
example of use of gene cloning
Ex. insulin production – insulin gene in bacterial plasmid which is then recombined with bacterial cell and propagated. The transformed bacterial cell can now produce insulin
134
who is responsible for the system to classify and name organisms
Carolus Linnaeus
135
Linnaeus original system
based on hierarchy
started with plants and animals
a third category was added later - protista
136
Linnaeus original system was first changed to
2 categories - prokaryote and eukaryote
137
The 2 category naming system was then changed to
```
5 kingdoms
monera
protists
fungi
plants
animals
```
138
in the 2 category system, monera are
bacteria
139
in the 2 category system, protists are
protozoans
| algae
140
the 2 category naming system was changed to
3 domains
eukarya
bacteria
archae
this is todays system
141
binomal nomenclature
first - genus
| second - species
142
genus
more general information
143
species
more specific information about the individual orangism or cell
144
scientific name is always
latinized
| underlined or written in italics
145
the genus is always
capitalized
146
the species is always
not capitalized
147
two categories that give the scientific nomenclature a problem
bacteria
| viruses
148
why are bacteria a problem for scientific nomenclature
The actual definition of species is that it is a group of organisms that share and can exchange genes from a common pool of genes – are capable of inbreeding
• Prokaryotes do not fit because they do not require breeding and exchanging of genes in their life cycle
149
new definition of species for bacteria
cells that have similarities within their member
150
who categorized bacterial species
Bergey
151
How did Bergey categorize bacteria
First by cell wall, then morphology, then biochemistry, serology
152
Bergey - cell wall
gram pos/neg
153
Bergey - morphology
shape/arrangement
154
Bergey - biochemistry
aerobic/anaerobic, carbon source
155
Bergey - serology
what antibodies are made in response to infection by it
156
Why are viruses a problem for scientific nomenclature
there is no evolutionary hx on them
157
how is viral naming different
their names are in English
they still have grouping by family, genus, and species
158
How do you begin in naming viruses
type of nucleic acid in their genome
159
types of viral genomes
ssDNA
dsDNA
ssRNA
dsRNA
160
Viruses are...
o Parasites
o Not cells
o Packages of genetic information
o So small cannot be seen under typical light microscope
161
viral replication
insert themselves into a host cell and use the host metabolic machinery to make more viruses
162
viral stages
replicating
| non-replicating
163
replicating stage
- inside host
| - called virus
164
non-replicating stage
- outside of host
| - called virion
165
a "virus" is in or out of a cell
inside
166
a "virion" is in or out of a cell
outside
167
schools of thought regarding viruses included
proliving
| antiliving
168
proliving support
o Viruses can evolve or adapt themselves to survive in a new environment
o Contain some macromolecules
o Can direct own reproduction
169
antiliving support
o Not cells
o Lack own metabolism
o In nonreplicating state show no obvious signs of life
170
ways to classify viruses
o Host range
o Size
o Structure
o Life cycle
171
What is meant by host range
viruses have a spectrum of organisms they will attack - some will attack plants, some animals, some eukaryotes, some only bacteria
172
what allows viruses to have a host range
every host cell has specific receptors on the surface that a virus recognizes and attaches to
173
virus size
1/10 to 1/3 the size of the smallest bacterial cell
174
virus structure
nucleic core surrounded by protein and sometimes a membrane
175
capsid
protein that surrounds the nucleic acid core of viruses
176
capsid shapes
helical
polyhedral
complex
177
polyhedral
20sided surface
178
complex
contains helical tail and polyhedral head
179
viral envelope
some have this membrane surrounding the virion
it is a piece of the host cell's plasma membrane that the virion acquired as it emerged from the host cell
180
how many steps are in the viral life cycle
6
181
viral life cycle
1. adsorb or attach to the host cell
2. viral genome enters the cell – penetration
3. virus loses its capsid – uncoating
4. manufacturing of viral components – viral synthesis
5. viral components assemble into new virions – maturation
6. virions are released from host, often killing it
182
what two steps of the viral life cycle often occur at the same time? in what type of virus do you see this most often?
penetration and uncoating
| bacteriophage
183
viral growth curve has...
two periods
184
periods of viral growth curve
latent
| burst
185
latent period
host cell is under the direction of viral nucleic acid and is producing components of new virions
186
burst period
the components assemble into new virions and release or burst from the host cell
187
typical amount of time for a virus to produce and release a large number of virions
40 minutes
188
average number of virions produced
200-500
189
developmental pathways of viruses
lytic
| lysogenic
190
first viral developmental pathway discovered
lytic
191
lytic pathway
virus produces new viruses and kills the host quickly
192
virulent phages are in the
lytic pathway
193
lysogenic pathway
Virus infects cell and inserts self into host chromosome – no viral components being produced at this time
Can be long quite time when host cell is maintained unharmed, reproducing itself
• As it reproduces, it copies the viral genome as well
When the host cell becomes stressed, the viral genome moves into the lytic path
194
temperate phages are in the
lysogenic pathway
195
difference between eukaryotic viruses and prokaryotic are found in
penetration
viral synthesis
releasing of virions
196
Ways of eukaryotic virus penetration
can happen in two ways
1. virion with an envelope can fuse with the host cell membrane
2. the host cell can be tricked into thinking the virus is something to eat, and the virus is endocytosed
197
What is needed if the viruses genome is RNA and it is infecting a eukaryote?
reverse transcriptase to allow it to transcribe its RNA into DNA which the host cell can then use to create more RNA
198
How are eukaryotic viruses released
lysis
| budding
199
budding
virions gently push their way out of the cell and take some of the membrane with them, which becomes the envelope
seen in eukaryotic
200
types of animal viruses
latent
retro
influenza
tumor
201
latent virus
Viral replication is arrested and the host cell functions normally for years
Ex. herpes and chicken pox
202
retro virus
Rna viruses that cause malignant tumors and leukemias in animals
Ex HIV
203
types of influenza
A
B
C
204
influenza A
* Most common
* Infect wide range of animals
* Known to cause pandemics, or worldwide epidemics
205
influenza B
* Only humans
* Appear in 2-3 year cycles
* Can be deadly
206
influenza C
* Only humans
| * Mild, cold-like illness
207
tumor virus
Cause uncontrolled growth of new tissue
| Ex. human T-cell leukemia, Burkitt’s lymphoma, Hep B
208
viroid
- Circular molecule of ssRNA without protein coat
| - Infects plants
209
symptoms of mad cow
o Aggressive behavior
o Muscle tremors
o Lack of coordination
o Death within months to a year
210
mad cow has a ___ incubation
5 year
211
CJ has a ___ incubation
up to 40 years
212
CJ spreads from
human to human
213
prion action
Causes DNA for the normal protein to mutate. One mutated, the cell produces the prion. The prion leaves the cell and moves to the next
214
another name for Mad Cow
bovine spongiform encephalopathy
215
ways CJ is transmitted
genetic
medical treatments
ingesting contaminated beef
216
how can we destroy prion
using bleach instead of water for autoclave
autoclave for 1 hour rather than 20 minutes
217
which bacteria make spores
gram positive
