Midterm 2 Flashcards
(182 cards)
1
Q
Macro composition in percent dry weights of protein, lipids, RNA, DNA, and saccharides
A
Protein: 55% Lipids: 9% RNA: 20% DNA: 3% Saccharides: 3-5%
2
Q
Which elements are needed to synthesize oxygen molecules?
A
Carbon
Hydrogen
Oxygen
3
Q
What are the 2 categories for carbon source organisms?
A
Autotrophs
Heterotrophs
4
Q
Autotrophs
A
Get their carbon from CO2
5
Q
Heterotrophs
A
Get their carbon from a source other than CO2
6
Q
What are the 2 categories for energy source organisms?
A
Phototrophs
Chemotrophs
7
Q
Phototrophs
A
Energy from light
8
Q
Chemotroph
A
Energy from oxidation of reduced compounds (organic or inorganic)
9
Q
What are the 2 categories for electron source organisms?
A
Lithotrophs
Organotrophs
10
Q
Lithotrophs
A
Get electrons from reduced inorganic compounds (eg. plants)
11
Q
Organotrophs
A
Get electrons from reduced organic compounds
12
Q
What is nitrogen needed for?
A
Amino acids Purines Pyramiding Cards Lipids
13
Q
What is phosphorous needed for?
A
Nucleic acids
Phospholipids
Nucleotides
14
Q
What is sulphur needed for?
A
Some amino acids
Some carbs
Biotin
Thiamine
15
Q
What is the reduced form of carbon?
A
CH4 (Methane)- Organic matter
16
Q
What is the oxidized form of carbon?
A
CO2 and CO
17
Q
What does CO2 fixation involve?
A
The conversion of CO2 into organic matter
18
Q
What type of organism would perform CO2 fixation?
A
Autotrophs (chemolithotrophy)
19
Q
What carries out nitrogen fixation?
A
Archae
Ex: Rhizobium
20
Q
Assimilatory reduction
A
Cytoplasmic
Not coupled to electron transport
Repressed by O2
21
Q
Dissimilatory reduction
A
Membrane bound
Coupled to electron transport
Repressed by ammonia
22
Q
What is the relationship between the carbon and nitrogen cycles?
A
They are coupled
23
Q
Prototrophic
A
Can make their own cofactors for enzymes
24
Q
Group translocation
A
Solute is modified as it is transported
25
What molecule assists in iron uptake?
Siderophore
26
Defined media
All components and amounts known
| Simple uses only 1 carbon source
27
Complex media
Specific amounts and composition not known
Usually contains digests of other organisms
Many are supportive media (allows growth of wide range of organisms)
28
Enriched media
Starts as complex, then other components added (ex: blood), for fastidious microbes
29
Selective media
Allows growth of some
| Inhibits others
30
Differential media
Allows for ID of bacteria based on colours, growth, or appearance of colonies
31
Ex of differential media
Eosin methylene blue agar
| -Identified lactose fermentors
32
What types of media is blood agar?
Enriched
| Differential
33
EMB agar is...
Selective
| Differential
34
Blood agar identified pathogens based on...
Hemolysis
35
Blood agar- Alpha
Green zone around colonies that signify incomplete hemolysis
36
Blood agar- Beta
Clear zone of complete hemolysis within a yellow colony
37
Blood agar- Gamma
No hemolysis (Clear)
38
How do you typically isolate a pure culture?
```
From stock solution
Dilute
Plate
Choose well-isolated colony
Replate
```
39
What are some features of ancient cells?
Some lack PTG wall
Must be osmotically protected
Do not divide by binary fission or use cytoskeletal proteins
40
What are all bacteria and archaea in regards to their genome?
Haploid
41
What are some points of binary fission?
Can be symmetrical- not always
| May involve formation of septum
42
What are the steps of binary fission?
Elongation
Septum formation
Cell separation
43
What are the 2 main points in the bacterial cell cycle?
1. Replication and partitioning of DNA
| 2. Cytokinesis
44
What direction is DNA replication in bacteria?
Bidirectional
45
5 steps of cytokinesis
1. Site selection
2. Assembly of FtsZ ring
3. Linkage of FtsZ ring to membrane
4. Assembly of synthesis apparatus
5. Constriction of cell, septum formation
46
What is FtsZ similar to in a eukaryotic cell?
Tubulin- Forms a ring that results in separation
47
What forms the divisome?
Fts proteins
48
What forms the ring?
FtsZ
49
What is FtsA similar to?
Actin (hydrolyzes ATP)
50
What anchors the ring to the membrane?
ZipA anchor
51
What do the min proteins do? (MinB)
Align the FtsZ ring
52
What is MreB similar to? What does it do?
Actin- Forms the helical simple cytoskeleton in bacteria and archaea
53
What is the region of new growth of the PTG layer called?
Divisome
54
What are 3 other forms of reproduction?
Budding
Spore formation
Baocyte formation (endospore)
55
Exponential growth
Number of cells doubles in a constant time interval
56
Generational time
g= t/n
| Duration of exponential growth divided by the number of generations
57
Division rate
v= 1/g
| Growth rate is another way to describe the division rate: Doubles per unit time
58
What are the 4 phases of the growth curve?
Lag
Exponential
Stationary
Death
59
What phase would you normally perform experiments on these cells?
Exponential
60
Batch culture
A closed system
61
Continuous culture
Open system; replenish nutrients, remove waste, will eventually reach equilibrium
62
What does nutrient concentration affect in a culture?
Growth and yield
63
What are direct counts for measuring growth?
Use a counting chamber (hemocytometer)
| Each chamber has a known volume- Count the cells and find the concentration (use a stain for viable cell counts)
64
What is flow cytometry?
Cells are fluorescently stained and then founded by their fluorescence- Can be used to sort too (FACS)
65
Coulter counter
Based on electrical flow
66
What is a disadvantage of plate counting?
Time- have to culture
67
What is optical density?
The light is being bounced off particles and measured
68
What are some disadvantages of OD counting?
Dead matter
Differing cell sizes
Only accurate over a narrow range
69
What are advantages of dry weight and OD readings for cell counts?
Simple, cheap, and fast, but they are an estimate
70
What are the 3 types of cardinal temperatures?
Minimum, maximum, and optimum
71
What effects where the cardinal temperature ranges lay for an organism environmentally?
Media and nutrient content
72
What happens at minimum temperature?
Membrane is gelling
| Transport is too slow to sustain life
73
What happens at maximum temperature?
Protein denaturation and collapse of membrane- Thermal lysis
74
What temp do enzyme catalytic rates double at?
10 degrees celsius
75
Psychrophile
Prefer colder temperatures
76
Mesophile
Prefer moderate temperatures (human body temp)
77
Thermophile
High temperatures (above 45)
78
Hyperthermophile
Prefer VERY high temperatures (above 80)
79
What class are hyperthermophile?
Archae
| Can survive autoclaves
80
Psychotrophs
Can grow at low, but prefer higher
81
What is the lowest temperature microbes survive at?
- 12 degrees
| - Psychromonas
82
What are some adaptations for cold temperatures?
Cold shock proteins and cryoprotectants
83
What are some adaptations for warm temps?
Heat stable proteins
| Special solutes in cytosol
84
What is pH?
-log [H+]
85
What are the 3 classes of external pH dwelling microbes?
Neutrophiles
Acidophiles
Alkalophiles
86
Neutrophiles
(5.5-7.9), most bacteria and protists
87
Acidophiles
(0-5.5), most fungi
88
Alkalophiles
(>8), most marine organisms
89
What is the internal pH range for all classes?
Cannot drop below 5, and is usually around 7
90
How do acidophiles stay neutral?
Transport cations into the cell, pump out H, highly permeable membranes
91
How do alkalophiles stay neutral?
Use Na instead of H to fuel transport
92
What is water activity (aw)?
Ratio of vapour pressure of air in eq with a solution to the vapour pressure of pure H2O
93
What is the aw of water?
1.0000
94
Halotolerant
0-5% salinity
95
Halophile
4-8% salinity
96
Extreme halophile
>15%- Actually require this amount of salt
97
Osmophiles
Live in high concentration of sugars
98
What are some adaptations for high solute concentration environments?
```
Mechanosensitive channels
Compatible solutes (sugars, OHs, AAs)
```
99
Where do aerobes grow?
The surface
100
Where do anaerobes grow?
Away from the surface
101
Where do facultative anaerobes grow?
Throughout media, but prefer the surface
102
Where do microaerophiles grow?
Just below the surface
103
Where do aerotolerant anaerobes grow?
Throughout, without any preference
104
What is ROS?
Reactive Oxygen Species- damages cells
105
What is ROS a byproduct of?
Respiration
106
How do cell combat ROS?
Have enzymes that break down ROS
107
Barotolerant
Can survive at high pressure
108
Piezophillic
Only survives at high pressure
109
How do microbes survive at high pressure?
Increased unsaturated fatty acids
110
What is a biofilm?
Non-motile extracellular polymeric substance, many species of bacteria and adherent to surfaces
111
What percentage of all bacteria live on biofilms?
80%
112
What are some pros of living in a biofilm?
Recycling of nutrients
Protection from stress
Biodiversity facilitated gene pool
Large gene pool
113
What are the 4 stages of a biofilm formation?
1. Attachment
2. Colonization
3. Development
4. Active dispersal
114
Biocide
A chemical or physical agent that inactivates microbes- broad spectrum
115
Sterilization
All cells, spores, and acellular entities destroyed or removed
116
Disinfection
Killing or severely inhibiting growth of microbes that may cause disease (surfaces/inanimate objects)
117
Decontamination
Treatment of an object making it safe to handle
118
Sanitization
Related to disinfection- level of microbes deemed safe by public health standards
119
Antiseptic
Chemical agent that kills or inhibits pathogenic microbes on tissues (generally not toxic)
120
Chemotherapy
Use of chemical agent to kill microbes within the host tissue
121
Decimal reduction time
Time required to kill 90% of microbes (one log cycle)
122
What is UV radiation good for?
Low amount of penetration- good for air and exposed surface and water
123
Where would we see UV radiation in use?
Meat packing
Biohazard cabinets
Water treatment
124
What is ionizing radiation good for?
Deep penetration
| Destroys spores- Not good at killing viruses, good for dry foods
125
Depth filter
Fibrous material in a think layer with small channels
126
2 types of depth filter
Berkfield (diatoms)
| Chamberland (unglazed porcelain)
127
Membrane filter
Porous
| Made with a variety of material of different pore sizes
128
HEPA filters
High efficiency particulate air filter- made of fibreglass, 0.3 um retention
Can filter out bacteria and viruses
129
Nucleopore filters
Made from polycarbonate, uniform in pore size - used for prepping samples in SEM
130
How does triclosan work?
Inhibits production of fatty acids - toxic to aquatic animals, hormone issues in rats
131
What does alcohol work against?
Bacteriacide and fungicide, does not kill spores
132
What is the best % to use in alcohol?
75%- if higher it causes shrinkage of the membrane and makes it hard to kill.
95% is used for flame sterile
133
How do phenolics work?
Denatures proteins, disrupts membranes
134
Why are phenolics so useful?
Remain active on surfaces for long periods, can kill mycobacteria (tuberculosis)
135
What do halogens work as?
Disinfectants and antiseptics
136
What is iodophore?
Water soluble iodine with organic component - releases iodine slowly to reduce irritation - used in hospitals to prep skin
137
What is silver nitrate used for?
Drops in newborns' eyes to reduce chance of infection
138
What is copper sulfate used for?
Preventing algal growth
139
What are quaternary ammonium compounds?
Detergents - good for skin and utensils, work well with phenolics, but not good in presence of organics
140
What do aldehydes act as?
Sporicides - Highly toxic and reactive
141
Why would you use sterilizing gas?
Good for sterilizing materials that cannot be heated
142
What is the difference between bacteriostatic and bactericidal?
Bacteriostatic- Stops growth, but doesn't kill (if you remove the agent, they will continue to grow)
Bactericidal- Will kill off cells, but won't get rid of the debris
143
What is MIC? How is it determined?
Minimum inhibitory concentration
| Dilution test
144
Diffusion test
Inoculate solid media
Add disks soaked in different bactericide
See which ones inhibit growth
145
Phenol coefficient test
Similar to dilution test, but compare the results to the efficacy of phenols
146
Catabolism
Breaking down material
147
Anabolism
Building large macromolecules from small precursors
148
Chemical work
Synthesizing molecules (anabolism)
149
Transport work
In/out of cell, or within- bacteria rely only on Brownian motion, whereas eukaryotes need energy input
150
Mechanical work
Movement- Convert chemical energy to physical energy
151
What is free energy and what does it do?
It is the energy available to do work, and it drives all reactions in the cell
152
What are conditions for the standard free energy?
pH of 7, 25 degrees, 1 atm pressure, 1M conc. of products and reactants
153
What does a negative free energy mean?
Exergonic - occurs spontaneously
154
What does a positive free energy mean?
Endergonic - does not occur spontaneously
155
How do you calculate standard free energy?
-RTlnKeq
156
What does G=0 mean?
The reaction is in equilibrium
157
What does the free energy under cellular conditions depend on?
Only on the G of reactants and products- provides no info on the rate of reaction
158
How do you calculate the free energy?
Standard free E + RTln (conc. products) / (conc. reactants)
159
How does ATP get used to drive reactions?
It conserves energy from exergonic reactions and this energy can then be used to drive endergonic reactions
160
What are metabolic pathways catalyzed by?
Enzymes and ribozymes
161
Why are redox reactions important?
They conserve energy
162
When you hydrolyze ATP what do you get?
ADP and orthophosphate (inorganic phosphate) + (-30.5 kJ/mol of energy)
163
What type of bond is very high energy?
Anhydride
164
What type of bond is very low energy?
Ester
165
How do enzymes increase reaction rate?
Stabilize transition state and lower activation energy
166
What do enzymes not change in terms of a reaction?
The free energy or the equilibrium constant
167
Who proposed the lock and key model?
Emil Fisher, 1890
168
Who proposed the induced fit model?
Daniel Koshland, 1958
169
What is methotrexate?
First chemo drug- a competitive inhibitor
170
How does penicillin work?
Suicide inhibitor for glycopeptide transpeptidase - does not allow cross linking of the PTG layer
171
What are the 3 methods of regulation of metabolism?
Metabolic channeling, amount of enzyme, enzyme effectors
172
What is metabolic channeling?
Compartmentalize substrates, or have them in a gradient
173
Why does feedback inhibition target the first step of a signal transduction or branch point?
Efficient, less wasteful (no intermediates), don't spend any more energy than needed
174
What is an allosteric enzyme?
The active site is separate from the regulatory site
175
What is allosteric regulation?
End product has different shape than starting product; can be used as a regulatory device for when the concentration of product becomes too high - the product can then bind to the regulatory site and inhibit the enzyme from reacting
176
Reducing agent
Electron donor
177
Oxidizing agent
Electron acceptor
178
Standard reduction potential (Eo)
The equilibrium constant that measures the tendency for the donor to lose electrons under standard conditions
179
How do we relate reduction potentials to standard free electrons?
Standard free E = -nF(standard reduction potential)
180
When looking at a redox tower, where are the oxidized and reduced forms?
Reduced on right, oxidized on left
181
If we have negative Eo, where does the equilibrium favour?
The oxidant
182
If we have a positive Eo, where does the equilibrium favour?
The reductant
