BIO 305 Exam 2 Chp 4-6 Flashcards
1
Q
What are the physical requirements for growth?
A
Temperature, pH, and osmotic pressure.
2
Q
What are the chemical requirements for growth?
A
Carbon, nitrogen, oxygen, hydrogen, sulfur, phosphorous, and other trace elements. (Most of the macronutrients).
3
Q
What are essential nutrients?
A
Essential nutrients=nutrients required for the growth that the organism cannot make on its own.
4
Q
What are macronutrients?
A
Macronutrients:
Carbon, nitrogen, hydrogen, oxygen, phosphorous, and sulfur.
Used a lot to make macromolecules.
5
Q
What are cofactors?
A
Cofactors are other important macronutrients but they are not used for macromolecules.
Mg2+, Fe2+, and K+ are important for enzyme function.
Ca2+ is a cofactor that acts as a secondary messenger.
6
Q
What are micronutrients?
A
Micronutrients=nutrients required for growth but only needed in small amounts.
Ex: Cobalt, zinc, and copper manganese.
7
Q
What are growth factors?
A
Growth factors=factors needed for some organisms to grow but not for all of them.
They may have evolved due to the organism’s environment and what it provides.
8
Q
What is defined minimal media?
A
Defined minimal medium=contains the minimum requirements for organisms to grow.
9
Q
What are obligate intracellular parasites?
A
Obligate intracellular parasites=those that are impossible to grow outside of the host.
10
Q
What is axenic growth?
A
Axenic growth=growth of a single organism in culture.
11
Q
How has metagenomics helped discover new organisms?
A
It shows new genetic material that does not match any known organisms. It shows uncultured organisms.
12
Q
What does LB Broth grow?
A
Gram-negative and Gram-positive cells.
13
Q
What does MP Medium grow?
A
Gram-negative cells like E. coli.
14
Q
What is proton motive force?
A
Proton motive force=moving of H+ across the membrane.
15
Q
How is the proton motive force useful in generation ATP?
A
It is the force and that causes protein changes and energy provider to anabolic build ATP.
16
Q
What are CFUs?
A
CFUs=colony forming units.
17
Q
While the assumption is that one cell=one colony, is that always true?
A
No. Some bacteria, like Staphylococcus, are bunched together so multiple cells form a colony.
18
Q
What are the important properties of agar that make it so useful?
A
Microbes can’t degrade it.
Liquefies at 100C.
Solidifies at 40C.
Once solidified, it will not become liquid until 100C again.
19
Q
What is the difference between streak plating and spread plating?
A
While both can use dilution, streak plating paints bacteria onto an agar plate so there are fewer bacteria with later streaks. Spreading plating lays bacteria on an agar plate by using liquid.
20
Q
What is sporulation?
A
Sporulation=formation of spores.
21
Q
What is germination?
A
Germination=return of a cell to a vegetative (growing) state.
22
Q
What does the suffix “-trophy” mean?
A
Trophy=acquistion of nutrients.
23
Q
What is a chemolitoautotroph?
A
Carbon source: reducing CO2.
Energy source: chemical reactions.
Electron source: Inorganic molecules.
Uses inorganic molecules for e-. Energy from oxidation is used to reduce CO2 for a carbon source.
24
Q
What is a photolithoautotroph?
A
Carbon source: reducing CO2
Energy source: Light.
Electron source: Inorganic molecules.
To capture energy from light, photolysis of inorganic molecules is used to excite their e-. The energy from capturing light is used to reduce CO2 for a carbon source.
25
What is a chemoorganotroph?
Carbon source: Digesting organic molecules.
Energy: Chemical reactions.
Electron source: Organic molecules.
Gain carbon and e- from an organic source. The e- from the organic source provides energy through chemical reactions.
26
What is a photoorganotroph?
Carbon source: Digesting organic molecules.
Energy: Light.
Electron source: Organic molecules.
Organic compounds are brought into the cell. Energy is gained from their breakdown through electrons and the absorption of light. Organic compounds are used to build biomass.
27
What do nitrogen-fixing bacteria do? What do they gain from this process?
Turn N2 into NH4 (ammonium). Nitrogen can now be integrated into organic molecules.
28
What do nitrifiers do? What do they gain from this process?
Nitrification=conversion of ammonia, or ammonium to nitrate (NO3-).
This is lithotrophy and they use ammonia and ammonium for electrons.
29
What do denitrifiers do? What do they gain from this process?
Denitrification=NO3- to N2.
| Reduce NO3- to N2 by using it as the final electron acceptor.
30
What is liquid media useful for?
Liquid media is useful for observing growth kinetics.
31
What is solid media useful for?
Solid media useful for isolating a single species.
32
What is complex media?
Complex media=components not defined, rich in nutrients.
33
What does complex media not tell us about the organisms growing in it?
Rich media does not allow us to know exactly what the organism needs to grow.
Since we don’t know exactly what is in it, we don’t know what growth factor they are relying on.
34
What is synthetic media? Do all organisms grow in it?
Synthetic media=components defined. No, because there may be missing growth factors.
35
What is defined media?
Defined media=media with only essential nutrients.
| Can be derived from synthetic media.
36
What is enriched media?
Enriched media=compoents of blood are added to media.
| These are for fastidious organisms.
37
What is selective media?
Selective media selects for one organism over another.
38
What is mannitol salt agar? What kind of media is it?
Selective media.
Mannitol salt agar has high salt conditions.
Ex: Promotes growth of Staphylococcus.
39
What is Sabouard’s dextrose agar? What kind of media is it?
Selective media.
Sabouard’s dextrose agar has a pH of 5.6 and is used to isolate fungi.
Used to grow yeast.
40
What is brilliant green agar? What kind of media is it?
Brilliant green agar=inhibits gram-positive and most gram-negative intestinal bacteria except for Salmonella.
41
What is differential media?
Differential media=selects for multiple organisms.
42
What is MacConkey agar? What kind of media is it?
Differentiating media.
Uses lactose as the differentiating part.
Uses bile salts to select for Gram-negative bacteria.
Gram-positive bacteria are less resistant to bile salts.
Distinguishes by color due to metabolism of different sugars causing a pH change.
There is a pH indicator in the media that shows a color difference among the different species.
43
Explain the Petroff-Hausser method of counting bacteria. Pros and cons?
Uses hemocytometer to count cells.
Very simple.
The count can be skewed by dead cells that are not distinguished from live cells.
44
Explain using fluorescent stains to count bacteria. Pros and cons?
Stains cells based on whether they are alive or dead. Ex: Propidium iodide, a red dye, intercalates in DNA but cannot penetrate the membrane of live cells.
Can distinguish between live and dead cells.
Equipment is expensive.
45
Explain the flow cytometry method for counting bacteria. Pros and cons?
Sorts cells based on expression levels of fluorescence which can be indicative of protein expression levels.
Can sort high expressing cells from low expressing cells.
Equipment is expensive.
46
Explain the viable count method for counting bacteria. Pros and cons?
Uses dilutions of bacteria on a streak or spread plate to find a number of CFUs.
Counts only living cells.
Takes time.
Not every CFU comes from one cell.
May underestimate the number of living cells. Damaged cells will be alive but cannot divide.
47
Explain the biomass method of counting bacteria. Pros and cons?
Dries out cells and weighs them.
Measures the overall size of a bacterial population.
Time-consuming.
Need a lot of mass because cells are so small.
48
Explain the biochemical assay method of counting bacteria. Pros and cons?
Measures protein content and metabolic rate.
More sensitive.
More accurate than biomass.
Some biochemical pathways fluctuate so the number will not always be the same and representative of how many cells there actually are.
49
What is the optical density method for counting bacteria. Pros and cons?
```
Uses spectrophotometer to measure how much light is absorbed by a dilution of culture.
Quick assay.
Cells can still get stuck together.
Constants are not perfect.
Only provides an approximate result.
Dead and live organisms scatter light.
```
50
Explain the PCR method for counting bacteria. Pros and cons?
Show quantification of DNA.
Doesn’t take too long to get results.
Dead and live cells have DNA.
51
What is the lag phase of growth?
Lag phase=little growth as bacteria get adjusted to the new environment and nutrient availability.
A lot of protein synthesis in this step.
52
What is the exponential phase of growth?
Exponential growth=great growth rate as bacteria grow and use up nutrients.
Bacteria are the most vulnerable here.
53
What is the stationary phase of growth?
Stationary phase=equal number of cells dying and growth.
Growth slows due to fewer nutrients.
Bacteria are more resistant here.
54
What is the death phase of growth?
Death phase=deaths outnumber growth.
| If media is not replaced, this will occur.
55
What is generation time/doubling time?
Time it takes for a cell to divide.
56
What are the steps for endospore formation?
Septum does not form in the middle of the cell, but closer to one of the poles.
Septum forms and forespore is created.
Replicated DNA is placed into the forespore.
Mother cell engulfs forespore.
The chromosome of mother cells disintegrates.
Exosporangium and protein cover are generated around the forespore for extra protection.
A layer of peptidoglycan is built between the forespore membrane and membrane made by the mother cell.
Spore coat includes calcium and dipicolinic acid is used to protect DNA.
Spore is released into the world.
57
What is the biofilm life cycle?
Some bacteria adhere to a surface.
The attached cells make a microcolony.
Biofilm gets larger and an exopolysaccharide (EPS) layer is formed for structure and protection.
A mature biofilm is generated.
Dissolution of biofilm occurs when nutrients become scarce.
58
What are the important aspects of a biofilm?
Exopolysaccharide layer=holds biofilm together.
Increased tolerance and resistance helps bacteria to survive.
Cell differentiation.
Different jobs based on where the cell is and what nutrients they have access to.
Cells that attach to a surface.
To keep biofilm attached to the surface.
Is the foundation for the rest of the biofilm.
Quorum sensing for communication.
Bacteria sense individually and do a respond as a group.
If bacteria can’t do quorum sensing, they can’t find a biofilm.
59
Explain the differentiation of cyanobacteria between oxygen-producing and nitrogen-producing bacteria.
For cyanobacteria species, (ex: Anabaena) every 10th cell becomes a heterocyst that fixes nitrogen.
The cyanobacteria must differentiate this job because the enzyme nitrogenase, which fixes bacteria, is very susceptible to oxygen and ROS.
Heterocysts have 3 extra cell walls and a special barrier to keep out O2.
60
What do fruiting bodies do? Explain their differentiation.
Fruiting bodies (such as in Myxococcus xanthus), form a biofilm under nutrient stress.
They are able to glide using pili.
Cells on the interior make spores that then spit out the biofilm.
The hope is that they will find a spot with better nutrients.
61
Explain the differentiation and life cycle of filamentous biofilms.
Filamentous biofilms can be formed with Anticomycetes species that generate filamentous hyphae that form mycelia. (This is similar to fungi).
Once a foundation in the soil is formed, aerial mycelia can be formed.
In high glucose time, exploratory cells will be sent to find the nutrient-rich areas.
In low glucose areas, aerial hyphae cells will be produced.
bld gene causes the production of aerial hyphae.
Once the growth stops, the spores of the aerial mycelial form.
The compartment segments of the aerial hyphae are formed from the whi gene.
62
How does ATP synthase work?
Uses protein motive force where H+ goes down its concentration gradient into the cell.
Proton motive force causes protein motor to spin and protein structural changes which allow for the construction of ATP.
This would not happen if energy were not provided for the change.
63
What is a symport?
Symport=molecules move in the same direction.
64
What is an antiport?
Antiport=molecuels move in different directions.
65
What is coupled transport?
A molecule moving down its concentration gradient provides energy to transport a molecule going up against its concentration gradient.
66
What is an ABC transporter?
ABC transporters=ATP-binding cassette superfamily.
| Uses ATP for active transport.
67
What is uptake active transport?
Uptake ABC transporters move molecules into the cell against their concentration gradient.
Uses a cognate to match a solute with a solute-binding protein to bring solutes to the ABC transporter.
68
What does cognate mean?
Cognate=matched.
| Ex: Siderophores that have a high affinity for iron and bring it to an ABC transporter.
69
What is efflux active transport?
Efflux ABC transporters move molecules out of the cell against their concentration gradient.
70
How is ATP used with ABC transporter?
ATP binds to ATP-binding cassette proteins on the ABC transporter.
Hydrolysis of ATP provides energy from uptake or influx.
71
How does group translocation work?
By chemically changing a product, you make it different so it can go down its concentration gradient.
It doesn’t match the normal solute on the outside and makes its own gradient with itself.
Ex: Phototransferase system with glucose to add a phosphate to it.
72
What is considered a normal environment? Temperature, pH, and osmolarity?
20-40C
pH=7.0
0.9% salinity.
73
What are extremophiles?
Extremeophiles=microbes that live outside of normal environmental ranges.
74
Does temperature increase always increase metabolism?
It does to a certain point because higher temperature means more molecular motion. However, for each cell's maximum temperature, enzymes and proteins will start to denature because it is too hot. When that happens, production goes down and the cell dies.
75
What are some reasons that cells might not want their proteins to all have the same temperature range?
The same enzymes are used in stress response.
Some only need to work in cold or hot temperatures.
Makes microbes more susceptible if everything has the same temperature range.
Not every protein has the same end goal.
Cells don’t want to grow as rapidly as possible because they would suck all their nutrients.
76
What are barophiles?
Barophiles (or piezophiles) can live at the bottom of the ocean where pressures reach 400-1,000 atm.
These bacteria are usually psychrophilic or thermophilic (if next to a heat vent).
Require intense pressure to survive.
77
What is water activity (a(w))?
Water activity (a(w))=availability of water.
78
What is osmolarity?
Osmolarity=concentration of solutes in solution.
79
What relationship do water activity and osmolarity have?
a(w) and osmolarity have an inverse relationship.
80
What are compatible solutes?
Compatible solutes=solutes that the cell can have a lot of with no negative effects.
81
What are mechanosensitive channels?
Mechanosensitive channels can release solutes when the pressure becomes too high.
82
What is plasmolyzing?
Plasmolyse=cell membrane pulls away from the cell wall and the cell lyses.
83
What are halophiles?
Halophiles require high salt.
| 2-4 M NaCl.
84
What are obligate halophiles?
Obligate halophile=require 30% salt solution to grow.
85
What are facultative halophiles (halotolerant)?
Facultative halophiles=can grow in high salt conditions but do not require it.
Can grow from 2%-15% salt.
86
What are strict aerobes?
Strict aerobes=need O2 to survive.
87
What are strict anaerobes?
Strict anaerobes cannot use O2 and do not have enzymes to remove ROS.
88
What are facultative aerobes?
Facultative microbes=can survive with and without oxygen.
| E. coli and yeast.
89
What are microaerophiles?
Microaerophilic=can withstand a small amount of O2.
90
What are aerotolerant microbes?
Aerotolerant=cannot use oxygen but can tolerate it well.
| Have enzymes to destroy ROS.
91
What makes oxygen so dangerous and toxic?
Makes free radicals that can harm cells by oxidizing reduced products.
Part of the aging process.
92
What is oxygen used for in aerobic respiration?
It is used as the final electron acceptor.
93
What does superoxide dismutase do?
Superoxide dismutase=ROS enzyme that turns O2- to H2O2.
94
What does catalase do?
Catalase=turns 2H2O2 to 2H2O and O2.
95
What does peroxidase do?
Peroxidase=turns 2H2O2 to 2H2O and NAD+.
96
What are reactive oxygen species?
ROS=H2O2, Superoxide (O2-), and hydroxyl radical.
Happens when oxygen is not completely reduced.
Mistakes are more likely to occur as organisms age.
97
How do anaerobes gain oxygen for their cell molecules?
Through eating sugars.
98
What are some ways to culture anaerobes?
Reducing media=liquid media that contains chemicals like sodium thioglycolate that combines with oxygen to deplete it.
Anaerobic jar and anaerobic chamber.
Tight-fitting lid and gas leak.
Can also use a jar with Petri dishes inside. Put a candle on top (that is lighted) and put a lid on top.
Candles will use up all oxygen.
Can use a glove port.
All bacteria stay inside with no oxygen.
Humans can interact through gloves in holes.
99
What does stress response to starvation entail?
Activates survival genes.
Metabolism slows, daughter cells become smaller, smaller signal molecules are produced and colony morphology changes.
Metabolism slows by switching nutrients it is using.
May take longer to break down.
Stress response genes are activated by second messengers and spores may develop.
100
How does apoptosis during starvation benefit cells?
The cell that dies does not benefit, but they release their nutrients into the environment for other cells to use and to prolong their survival.
101
Explain the E. coli MazEF Toxin-Anti-toxin system
MazE=anti-toxin.
Less stable than toxin.
MazF=toxin.
More stable.
In stress, production of both stops.
MaxF can survive longer and is free to cleave mRNA.
Cells can release G6PD (Glucose 6 phosphate dehydrogenase) and can inhibit MazE in other cells.
Does not kill the whole colony because the amount of G6PD is less than the amount of nutrients.
102
What is eutrophication?
Eutrophication=increase in formerly limiting nutrients.
103
What is sterilization?
Sterilization=destruction of all forms of microbial life, including endospores.
104
What is disinfection?
Disinfection=killing harmful microbes.
| Can use chemicals, ultraviolet radiation, or boiling water.
105
What is antisepsis?
Antisepsis=treatment of living tissue to remove harmful microorganisms.
Antiseptic=chemical for antisepsis.
106
What is sanitization?
Sanitization=killing most of the microorganisms in a limited area.
107
What does the suffix "-cide" mean?
“-cide”=killing.
108
What does the suffix "-stat" or "-stasis" mean?
“-stat” or “-stasis”=inhibiting or slowing growth.
109
What does sepsis mean?
Sepsis=indicates bacterial contamination.
110
What does aseptic mean?
Aseptic=without contamination.
111
What does asepsis mean?
Asepsis=absence of significant contamination.
112
What is the D-value?
D-value=decimal reduction time; the amount of time to get 90% reduction when killing cells.
Cells die at a logarithmic rate.
113
How do control agents kill cells?
Alterations in membrane permeability.
Damage to lipids or proteins that make up the plasma membrane can cause cellular content to leak or interfere with cell growth.
Damage to protein and nucleic acids.
Damage to DNA or proteins can easily lead to the death of the cell.
114
What are hyperthermophiles?
Temperature 80 C+.
115
What are thermophiles?
Temperature 50-80 C.
116
What are mesophiles?
Temperature 20-40 C.
117
What are psychrotrophs?
Tolerant of temperature from 0-7 C but optimal is 20-35 C.
118
What are psychrophiles?
Temperature below 15 C.
119
What are alkaliphiles?
pH=9+.
120
What are neutralophiles?
pH=5-8.
121
What are acidophiles?
pH below 3.
122
What are barotolerant microbes?
Can tolerate pressure from 10-495 atm.
123
How do microbes survive extreme temperatures?
High temperature:
Fewer glycine since it is an amino acid susceptible to temperature.
More saturated fatty acid tails to have a more rigid membrane.
Proteins and enzymes that can survive in the higher temperature without denaturing.
More H-bonds make them harder to denature.
More DNA binding proteins to keep DNA from denaturing.
Can use more chaperone proteins to help other proteins fold.
These proteins are used in heat shock response for other microorganisms.
For low temperatures, membranes are more flexible proteins and membranes that require less energy.
124
How do microbes survive extreme pressure?
Decrease membrane fluidity.
| Barophiles also have to deal with low temperature or high temperature (if they are next to a heat vent.
125
How do microbes survive extreme salt conditions?
Pump in K+, and pump out Na+.
Enzymes actually require a high concentration of K+.
In temporary high salt conditions, microbes can use chaperone proteins to keep their proteins from denaturing.
In hypotonic, they use mechanosensitive channels that pump out solutes to lower intracellular pressure.
In hypertonic solutions, can pump in a lot of compatible solutes that the cell can tolerate.
126
How do acidophiles survive their extreme pH conditions?
Pump in K+.
Scientists are not sure how this helps them survive, but it does.
Altered membranes to keep out H+.
pH optimum of proteins does not change because these strategies maintain a different internal pH.
127
How do alkaliphiles survive their extreme pH conditions?
Effective iron transport proteins because there is so little soluble iron in that environment.
Use Na+/H+ antiports to survive in basic pH.
Uses Na+ motive force as well as H+ motive force.
Excreted enzymes can handle the high alkaline environment.
pH optimum of proteins does not change because these strategies maintain a different internal pH.
128
How does the autoclave kill microbes?
High pressure, high temperature.
Uses steam.
High pressure can raise the temperature.
Temperature goes up to 121 C.
Can sterilize whatever goes in the autoclave.
129
What is LTLT Pasteurization?
LTLT=low temperature; long time.
| 62 C for 30 minutes.
130
What is HTST Pasteurization?
HTST=high temperature; short time.
| 72 C for 15 seconds.
131
What is UHT Pasteurization?
UHT=ultra-high temperature.
134 C for 1-2 seconds.
This can increase the shelf stability of milk.
132
How does filtration control microbes?
Filters must be smaller than 0.2 um to remove most bacteria.
Still too big for viruses.
Fume hoods remove pathogens from the air.
133
How can cold control microbes?
0-7C can be used to slow or stop growth.
Refrigerators have a bacteriostatic effect.
Slow freezing will kill bacteria more than snap freezing.
The reason is that ice crystals will kill them.
134
How does irradiation kill the cell?
When irradiated, water, DNA, proteins, and other cell compartments absorb the energy and form short-lived harmful substances (usually ROS) that kill the cell.
135
What is ionizing radiation?
Ionizing=more energy; wavelength less than 1 nm.
Ex: X-rays.
Can penetrate much more deeply than non-ionizing radiation.
136
What is non-ionizing radiation?
Non-ionzing=less energy; wavelength greater than 1 nm.
Ex: UV light.
Great for mutating DNA.
Links thymine nucleotides inhibiting correct DNA replication.
137
Why does the amount of radiation energy differ to kill cells?
Depends on the size of its genome, nucleic acid:cell ratio, and how fast it can repair the DNA.
Eukaryotes take fewer Grays to kill because their cells are bigger with less genome:cell ratio.
Viruses are hard to kill because they do not have water, the greatest ionizing agent for irradiation.
Prions are the hardest to kill because they do not have any nucleic acids.
138
Why is Deinococcus radiodurans such an interesting species when talking about radiation treatment?
```
Deinoccous radiodurans can survive radiation even up to an atomic blast.
Extreme robust DNA repair enzymes.
Has a lot of manganese.
Manganese can detoxify radicals.
Can use it for bioremediation.
Specifically for nuclear areas.
```
139
What are the factors that influence the effectiveness of a chemical agent?
Microbe number and type.
The more microorganisms, the longer it takes to kill.
Environmental influences: the presence of organic matter often inhibits an antimicrobial because it traps it or slows it down.
Corrosiveness: The antimicrobial should not corrode the surface or skin.
H2O2.
Reacts with everything.
Stability, odor, and surface tension: should be stable and neutral to be the most effective.
140
What is the Minimal Inhibitory Concentration (MIC) test?
You observe a microbe's normal growth curve. You add a chemical agent and see how the growth curve changes. You are trying to find the smallest concentration that will inhibit growth.
141
What is the use-dilution test?
Metal carrier rings dipped in standardized liquid cultures and dried at 37 C.
Then placed in the disinfectant for 10 minutes at 20 C.
Rings are placed on the growth medium and observe the growth.
142
What is the disk-diffusion test for evaluating a chemical agent?
A disk of filter paper is soaked with disinfectant.
Placed on a lawn of organisms of interest.
The zone of inhibition (loss of growth) can be measured and quantified.
Disks containing antibiotics are commercially available.
143
What is the phenol coefficient?
Made by Joseph Lister.
Used as a benchmark for disinfection.
Higher the coefficient, the higher the efficacy.
Phenol is no longer used because it kills everything around it.
144
What are phenolics?
Derivatives of phenol that are less toxic.
| Ex: Lysol that uses o-phenylphenol.
145
What is a tincture?
Alcohol + whatever else you are using.
146
Why is the optimum concentration of alcohol 70%?
Alcohol needs some water so that it can enter cells.
147
What are biguanides as a chemical control agent?
Biguanides have a broad-spectrum effect.
Ex: Chlorhexidine.
Biocide for most bacteria but not Mycobacteria, endospores, and protozoan cysts.
148
What are halogens as a chemical control agent?
Ex: Iodine and chlorine.
Very effective.
Effective against bacteria, fungi, endospores, and viruses.
Betadine=most common iododine.
A gaseous form of chlorine (ClO2) is used to disinfect an area and kill Anthrax spores.
149
What are alcohols as a chemical control agent?
Kill by protein denaturation.
| Does not kill endospores and nonenveloped viruses.
150
What are heavy metals as a chemical control agent?
Ex: Silver, mercury, copper, cadmium, and zinc.
Can be biocidal.
Copper surfaces are being used in hospitals.
1% silver nitrate to treat gonorrhea-causing bacteria in the eyes of newborns.
Copper sulfite is used to clean up green algae (algicide) from reservoirs, pools, and fish tanks.
Can clean up water supplies in low concentration.
151
How can microbes gain resistance to chemical agents?
Resistance is much more likely if the agent only has a few targets.
Efficient multi-drug efflux transports like Pseudomonas.
Biofilm formation.
152
What are antibiotics?
Antibiotics=naturally made chemical compounds by one microbe to kill another microbe.
153
What are some ways that bacteria avoid suicide by their own antibiotic?
Not having the target molecule.
Modify its receptors to not recognize the molecule.
Modifies the antibiotic if it reenters the cell.
Uses enzymes.
Expresses the resistance gene to the antibiotic as well.
154
Why is antibiotic resistance so rampant?
Antibiotics usually have very specific targets so they are easier to gain resistance to.
155
What are bacteriophages?
Viruses that impact bacteria.
156
What are the general structural components of a virus?
Genome, capsid, possible spike proteins or extracellular proteins, possible envelope, and tegument (space between capsid and envelope) if an envelope is present.
157
What are viroids?
Infectious materials that have no capsid, just a genome.
158
What are spike proteins?
Proteins made of glycoprotein that stick up from the virus. Can be used for identification. Can hold capsid and envelope together. Can be used for attachment.
159
What does icosahedral mean?
20-sided capsid.
160
What is a filamentous virus shape?
Symmetrical helical shape. Both capsid and genome could be helical. Longer than it is wide.
161
What are asymmetrical viruses?
Asymmetrical viruses can have asymmetrical genomes with multiple “chromosomes” or an asymmetrical shape (ex: oval).
162
What do all viruses need to replicate?
A host.
163
What is the RNA world hypothesis?
RNA world=RNA did everything before DNA came along.
| Stores information, is structural and is functional.
164
What is a virus?
Virus=noncellular dynamic particle that infects a host cell to reproduce.
165
Who discovered tobacco mosaic disease?
Iwanowski and Beijernick discovered tobacco mosaic virus (TMV).
166
Who isolated tobacco mosaic virus (TMV) for chemical and structural study?
Stanley in 1935.
167
Who sequenced the first viral genome?
Fred Sanger. He also developed the Sanger method for sequencing.
168
What is a host range?
Host range=number of hosts that a virus can infect.
| Can be broad or narrow.
169
What does promiscuous mean in relation to viruses?
Promiscuous=virus hopping around different hosts.
170
What is a prophage?
Prophage=viruses integrated into the bacterial genome.
171
What is a provirus?
Provirus=virus integrated into the human genome.
172
What is an endogenous virus?
Endogenous viruses=viruses that get to the germ cells and are passed on to offspring.
173
What are some positive things that viruses do?
Contribute to nutrient cycling, get rid of microbial blooms, and mediate host population control.
174
What does limit host density due to the spread of viruses?
Limits transmission because there are fewer hosts in a given area that viruses can infect.
175
How is monoculture good for viruses?
Lots of near-identical hosts in an area.
| This is a con for monocultures for agriculture
176
What is a viral shunt?
Viral shunt=batch of nutrients that fall to the ocean floor after viruses destroy algal blooms.
Can recycle nutrients.
177
What is a capsid?
Capsid=container for viral genetic material.
178
What is a plaque?
Plaque=clear spot in a lawn of cells.
| Due to lysing of the bacteria due to a phage.
179
What is the purpose of viruses having an envelope?
The envelope is usually from the host. Having the envelope means the cell can have an easier time getting into the cell.
180
How can integrated viral genomes be beneficial?
They can provide resistance to toxins and environmental factors.
For humans, some endogenous virus translates to essential proteins in the placenta.
181
What is the intracellular replication complex?
Inside the host cell, the virus recruits the cell’s proteins in the replication process to replicate the viral genome.
182
What are some giant viruses thought to originate from?
Thought to originate from cells, maybe obligate intracellular cells, that underwent reductive evolution.
183
What are tailed viruses?
The genome is connected to a helical neck that delivers the genome to the host cell.
Six jointed legs stabilize the virus on the host cell.
184
What are prions?
Prions=aberrant infectious proteins.
Unaffected by treatments that target RNA or DNA.
Includes nucleases and UV radiation.
Prions bind to normal proteins and then change their shape to the prion’s shape.
185
Describe dsDNA viruses.
Uses its own or hosts’ DNA polymerase for replication.
RNA polymerase can also come from the virus or the host cell.
Group 1.
186
Describe ssDNA viruses.
Uses hosts’ DNA polymerase to replicate the strand.
Double-stranded DNA can then be read by the hosts’ RNA polymerase.
Group 2.
187
Describe dsRNA viruses.
Require RNA-dependent RNA polymerase to make mRNA.
A virus may package an RNA polymerase before it leaves the host cell.
Ex: Reoviruses.
Includes rotavirus which causes diarrhea in children.
Group 3.
188
Describe + RNA viruses.
Single-stranded.
Contains + sense strand, the coding strand.
Still needs RNA polymerase to be replicated.
Cannot make more + strand without the - strand.
Can serve as mRNA to make proteins.
Includes coronaviruses.
Group 4.
189
Describe - RNA viruses.
Single stranded.
Contains the - strand which needs to be replicated before translation can occur.
Need to package viral RNA-dependent RNA polymerase.
Often segmented.
Ex: Influenza.
Group 5.
190
Explain retroviruses.
+ ssRNA.
Has reverse transcriptase which transcribes RNA into double-stranded DNA.
Integrated into the host genome.
Group 6.
191
Explain pararetroviruses.
Has double-stranded DNA.
Transcribes to RNA.
Then, uses reverse-transcriptase to turn RNA back to progeny DNA.
Reverse transcriptase is packaged into the virion.
Group 7.
192
Explain the lytic viral replication cycle.
The virus recognizes the host and attaches to it.
Genome must enter the host cell.
Viral phage progenies must be constructed.
Phage progenies must exit the cell to infect new hosts.
They lyse and break open the host cell as they do this.
193
Explain the lysogenic viral replication cycle.
The viral genome integrates with the host genome.
Usually site-specific.
The viral genome can cut itself out of the genome and turn back into the lytic cycle if environmental conditions or host health deteriorates.
194
What kinds of viruses do the slow-release viral replication cycle?
Filamentous ssDNA viruses.
195
Explain the slow-release viral replication cycle.
Able to enter and exit the cell without killing it.
Single-stranded DNA is made into double-stranded DNA.
Double-stranded DNA slowly forms single-stranded viral progeny.
Uses negative supercoiling.
The virus, with the capsid, leaves the host cell alive.
The host cell is alive but grows and replicates more slowly than uninfected cells.
This is because the virus production took a lot of the host cell’s nutrients.
196
List the great variety available for viral genomes.
RNA or DNA.
For RNA, can be + or - based on whether it is the sense or antisense strand.
Can be single or double-stranded.
Can be linear or circular.
Whole or segmented.
Segmented=separated into separated “chromosomes”.
197
Why can't viruses be categorized by gene-relatedness or host type?
There is such a great variety in genomes that viruses with different genomes may be more closely related. Viruses of different hosts may be more similar than viruses with the same host.
So, to categorize viruses, they are categorized by the type of genome they have and relatedness is determined by the proteome.
198
What are orthologs?
Orthologs=genes of common ancestry that share the same function.
199
What are coliphages?
Coliphages=gut bacteriophages.
200
How can surface proteins change resistance to viruses?
The cell surface receptors that viruses bind to are very specific. A host can gain immunity by changing its cell-surface proteins.
201
What is a ghost?
Empty capsid once the genome has been inserted into the cell.
202
What is burst size?
Burst size=size of virus progeny that leave a lysed host cell.
203
What is dsDNA?
dsDNA=double stranded DNA.
204
What's the difference between early genes and late genes?
Early genes are viral genes that are expressed soonest after translation. Closest to the beginning of translation point. Usually translates for polymerases and transcriptase to continue replication and translation.
Late genes are expressed at the end. They usually code for proteins that will lyse the host cell.
205
What is transduction?
When a virus takes some of the host's cell DNA with it.
206
Explain how the CRISPR system acts as an immune system for bacteria.
When the cell can destroy phage DNA, some of it goes into the CRISPR system to be remembered.
CRISPR DNA becomes crRNA.
crRNA binds to the Cas protein complex.
This complex looks for analogous RNA that binds to genetic material from viruses.
207
What is the Arc system some viruses use to counteract CRISPR?
Phages have evolved anti-CRISPR proteins called Arc.
Can bind to the Cas system which prevents it to bind to viral genetic material. Therefore, the CRISPR system does not go off.
208
How does uses restriction endonucleases protect bacteria from viruses?
Bacteria put methyl groups on some of their bases.
Restriction endonucleases cut DNA without these methyl groups.
Viral DNA genomes do not have these methyl groups so they go off.
209
How do some viral genomes escape detection by restriction endonucleases?
Viruses with changed genomes such as RNA to DNA escape the restriction endonucleases because in the reverse transcription process methyl groups are added.
210
What are the 3 main ways that bacteria have resistance to viruses?
```
Genetic resistance (ex: mutations)
Restriction endonucleases.
CRISPR.
```
211
What is a virome?
Virome=community of viruses in a host.
212
What is transcytosis?
Transcytosis=human tissue taking up bacteriophages.
213
What is dysbiosis?
Dysbiosis=deterioration of health due to loss of health-promoting bacteria.
214
What are some hypotheses for why transcytosis occurs?
Because viruses are inert when not in a host, human cells may move bacteriophages around to help them find hosts.
Having phages inside human cells can provide defenses against bacteria that enter the human cell.
215
How can phages in the gut biome be useful?
Bring equilibrium in bacteria numbers to what the human gut can tolerate.
Can modulate the immune system.
Attack biofilms.
Can transfer use genetic material to hosts.
216
What is tropism?
Tropism=ability for viruses to affect different tissues in eukaryotic multicellular organisms.
Viruses can have a broad range (like Ebola) or a narrow range (like polio).
217
What is uncoating for viruses?
Uncoating=process by which the capsid comes apart.
| Can happen in the cytoplasm or at a specific organelle.
218
What are ways that viruses enter animal cells?
The viral membrane binds to receptor proteins and becomes part of the cell membrane.
The genome enters directly into the cytoplasm.
Viruses can be encoded in an endosome.
Endosomes can be broken up by a lysosome, and the genome enters the cytoplasm.
Or endosomes can bring the virus to a specific organelle, like the nucleus.
In the nucleus, viruses can take advantage of DNA polymerase, DNA binding proteins, and transcription factors.
219
What is an episome?
Episome=DNA that can live autonomously in the cell (like plasmids) or be integrated into the genome.
220
How can viruses cause cancer?
Oncogenes.
Can encode for abnormal oncogenes that deregulate growth.
Genome integration.
Viruses can encode for factors that stimulate host cell division.
Cell cycle control.
Express viral proteins that mess with host cell cycle controls.
221
In animal cells, what are the two places where viral assembly most likely takes place?
At the ER and the nucleus for nuclear virions.
222
How is it beneficial for viruses to cause host cells to become cancerous?
This is beneficial because the more offspring the host has, the more cells now carry the virus. More viral progeny can be made.
223
How can low-level chronic viral infections enhance the immune system?
The immune system has to be active and fight infections to gain a better memory and do better at its job.
224
How do viruses infect plant cells?
Viruses enter through damaged tissue.
Animals that eat plants cause damage and can transmit viruses that way.
Some enter the seed and can infect the next generation.
Enter through plasmodesmata (cell junctions that connect cells). Usually not the first mode of entry but how uninfected cells get infected.
225
Why can't plant viruses just enter through the cell wall?
Too thick and hard to penetrate.
226
What are animal and plant defenses against viruses?
Genetic resistance through mutations.
Harder for animals and crops in monoculture.
Immune system.
Interferons=immune system particles that recognize viral particles such as dsRNA.
The immune system has antibodies to recognize certain viral proteins.
RNA interference:
When translating mRNA, the host RNA complex can recognize the viral RNA and refuse to translate it.
227
Why must viruses be cultured with a host?
Because viruses cannot be cultured on their own.
228
What is batch culture?
Batch culture=liquid culture that allows the growth of a large number of viruses.
229
What is multiplicity of infection?
Multiplicity of infection=virus to host cell ratio.
| Can manipulate it to make sure every host cell is infected.
230
In viral growth curves, what is the eclipse phase?
Eclipse phase=time when no virus progenies are made.
| The viral genome is still being delivered.
231
In viral growth curves, what is the latent phase?
Latent phase=viral progeny have been made but have not yet burst out of the cell.
Easier to see in animal cells because virus progeny usually buds out of the cell.
232
What is the difference between latent phase and latent infection?
Latent phase=viral progeny have been made but have not yet burst out of the cell.
Latent infection=when a virus maintains its genome in the cell but does not produce any virions.
233
In viral growth curves, what is the rise phase?
Rise phase=increase in viral progeny from host cells.
234
What is a lysate?
Lysate=viral particles in suspension.
235
What is virulence?
Virulence=ability to cause disease.
236
Why is the burst sizes for animal cells bigger than burst size for bacterial cells?
Animals cells are larger and have more resources to make more virions.
237
What are plaque-forming units (PFUs)?
Plaque forming units (PFUs)=by counting the number of plaques, we can estimate how many viruses there are.
238
How are viruses cultured in bacteria?
Seen by PFUs. Can generate a lysate for the virions in the burst size.
239
Why does the method for culturing animal viruses different than culturing viruses from bacteria?
Animal cells are cultured with liquid on top. You could not count the number of plaques because released virions would spread throughout the plate via the liquid.
240
What is a method for culturing animal viruses?
Infect monolayer.
Allow enough time for viruses to latch onto the host.
Remove liquid layer (aspirate it).
Add gelatin layer.
This will still allow host cells to grow but limit the dispersal of viral progeny.
241
What are focus methods for culturing animal viruses?
Focus methods are used for cells that are infected by a virus that does not kill them.
Can be visualized by fluorescence using an antibody.
Can be visualized by piles of transformed cells that have infected with oncogenic viruses that turn host cells into cancer cells.
