Exam 2 Flashcards
1
Q
Required macronutrients for growth
A
carbon, nitrogen, phosphorus, sulfur, hydrogen, and oxygen
2
Q
Required micronutrients for growth
A
Mn, Zn, Co, Ni, Mo, and Cu
3
Q
What macronutrient is found in the highest quantity?
A
carbon
4
Q
What do all organisms require?
A
carbon, hydrogen, oxygen, and electrons
5
Q
Autotrophs
A
they assimilate carbon from inorganic sources
6
Q
Heterotrophs
A
they assimilate carbon from organic sources
7
Q
Phototrophs
A
they capture light energy to produce ATP
8
Q
Chemotroph
A
they capture energy from outside or inorganic compounds
9
Q
Organotrophs
A
they acquire their electrons from organic molecules
10
Q
Lithotrophs
A
they acquire their electrons from inorganic sources
11
Q
Mixotrophs
A
they have great metabolic flexibility and alter their metabolism in response to environmental changes (advantageous)
12
Q
What is nitrogen needed in?
A
amino acids, purines, pyrimidines, some carbohydrates, lipids, enzyme cofactors, and proteins
13
Q
How can nitrogen be obtained?
A
can be obtained by breaking down their molecules that contain nitrogen and then nitrogen can be used once it is released
14
Q
Nitrogen fixation
A
the nitrogen comes as ammonia then nitrogen separates into air which can be used
15
Q
What is phosphorus needed in?
A
nucleic acids, phospholipids, coenzymes, and some proteins
16
Q
What is phosphorus found in?
A
in inorganic phosphate and organic molecules containing a phosphoryl group, important for membrane production
17
Q
What is sulfur needed in?
A
amino acids (cysteine and methionine), coenzymes, sulfate which uses assimilatory sulfate reduction (sulfate to sulfite to hydrogen sulfide)
18
Q
Growth factors
A
organic compounds that cannot be synthesized by an organism but are essential for growth
19
Q
What are the 3 classes of growth factors?
A
amino acids (protein synthesis), purines/pyrimidines (nucleic acids synthesis), and vitamins (enzyme cofactors, needed in very small amounts)
20
Q
How does nutrient concentration relate to growth?
A
it is dependent on the amount of nutrients in the environment, one key nutrient available in the lowest amount will dictate how much growth can occur over time
21
Q
Why is oxygen important in growth?
A
effects of oxygen on microbial growth is determined by what defenses are available against oxygens’ negative effects in cells
22
Q
Aerobes
A
grow in presence of oxygen
23
Q
Obligate aerobes
A
require oxygen
24
Q
Microaerophiles
A
grow best when there is less oxygen than normal
25
Anaerobic growth
occurs without oxygen
26
Aerotolerant anaerobes
not harmed by oxygen but do not use it either
27
Obligate anaerobes
cannot grow when oxygen is present
28
Facultative anaerobes
use oxygen but also grow in the absence of oxygen
29
What is ROS?
reactive oxygen species
30
What are the enzymes that protect against toxic oxygen?
superoxide dismutase for hydrogen peroxide reaction, catalase for superoxide radical reaction and peroxidase
31
What do strict anaerobic microorganism lack for enzymes?
superoxide dismutase and catalase
32
How can oxygen be removed in lab?
gaspak anaerobic system or anaerobic workstation with an incubator
33
Anaerobic workstation with an incubator
That is much more permanent, the plates/tubes are put into an airlock and the door is sealed. The work is done with glove locks by putting hands in gloves. The oxygen is removed once the door is sealed with a vacuum and then basically the oxygen is replaced with nitrogen gas with hydrogen and palladium catalysts. Carbon dioxide can put in for the anaerobic process
34
What do palladium catalyst do?
they hydrolyze a reaction between hydrogen gas and any remaining oxygen atoms that remain in the system
35
Gaspak anaerobic system
It is more of a temporary system, the bucket is opened by the lid then the plates are placed inside. Once the lock screw is on, the rubber gasket seal starts to remove oxygen. There is a catalyst chamber that contains palladium pellets. The hydrogen gas comes from the gas oak envelope which transmits hydrogen and carbon dioxide. There is no nitrogen exchange so only the gaspak does the work. When all of oxygen is out of system of the system, the indicator strip will turn colorless
36
Acidophiles
have a pH of 5.5 or less
37
Neutrophiles
optimal pH of 5.5 to 8.5
38
Alkaliphiles
have a pH of 8.5 or more
39
What is the optimal temperature for domain archaea?
extreme temperatures
40
Psychrophiles
0-20C
41
Psychrotrophs
0-35C
42
Mesophiles
20-45C
43
Thermophiles
55-85C
44
Hyperthermophiles
85-113C (deep sea vents)
45
What are adaptations of thermophiles?
protein structure stabilized by variety of means like hydrogen bonding, more prolines since they are more rigid, more charged amino acids, chaperones which bind to proteins and prevent them from moving. use histone-like proteins to keep DNA round up tightly. membrane stabilized by ether linkages, higher levels of saturation
46
How are the membranes like in lower temperatures?
lower levels of saturation and enzyme functionality with less energy
47
What are the solutions for hypotonic conditions?
cell wall and some bacteria have mechnosentive channels which detect the overstretching of the membrane by moving things in and out of the cell to prevent the burst from happening
48
Water activity
the degree of water available to the cell
49
How can water availability be changed?
drying, adding solute, and adding salt
50
Halophiles
evolved to live in hypertonic environments, can grow optimally in the presence of NaCl or other salts at concentration above about 0.2M
51
Extreme halophiles
require salt concentration of 2M to 6.2M
52
How are halophiles able to survive?
with compatible solutes (salts that do not damage the cell in any way) that can be kept at high internal concentrations so water will not want to move anywhere
53
Non-halophiles
do not like salts so 0.2M salts is their optimal growth (too much salt will kill them) and do not have a defense mechanism that protects the water from leaving the cell
54
Moderate halophiles
need to have salt in order to grow and their optimal growth is about 2M
55
What do culture media allow us to do?
distinguish different bacteria and allow the growth of bacteria
56
How is the culture media classified?
chemical constituents, physical nature, and function
57
Complex media
everything is in a big mix
58
Defined media
media is coming from a specific place
59
What is the first media you should try?
complex if you have no information about the bacteria
60
What media should you try to find nutritious information?
defined media
61
What are important complex media components?
peptones, extracts, and agar
62
Peptones
protein hydrolysates prepared by partial digestion of various protein sources, good sources of carbon, nitrogen, and phosphorus
63
Extracts
aqueous extracts usually of beef or yeast
64
Agar
sulfated polysaccharides used to solidify liquid media and most microorganisms cannot degrade it - usually extracted from red algae
65
Functional media types
enriched, selective, differential
66
Supportive media
additional nutrients that favor a particular microbe
67
Selective media
select the growth of a selective bacteria and then it inhibits the growth the another microorganism
68
Differential media
differentiate between different bacteria types on a plate, their biological feature, and can distinguish between which species as well
69
MacConkey agar
selective and differential media type because it contains bio salts, and select the growth of gram-negative
70
Why does MacConkey agar inhibit the growth of gram-positive bacteria?
bio salts come into the membrane an attack and inhibits all movements
71
Blood agar
enriched media but is also differential and is used to differentiate bacteria based on hemolytic properties
72
Chocolate agar
blood agar that has been sliced
73
3 basic techniques for isolating colonies
plate streaking, pour plating, and spread plate
74
Plate streaking
spread mixture of cells on agar surface for good separation using a sterilized loop to spread colonies
75
Pour plate
adding diluted bacteria to molten agar medium and pour into plate and let incubate, the colonies appear not only on the surface but also within, some bacteria might die with the molten agar
76
Spread plate
pour bacteria suspension onto solid agar medium and spread with glass rod then let incubate, motile bacteria can move
77
How do we gain information about unculturable bacteria?
DNA can be amplified and sequenced by PCR and sequences can be used to produce fluorescent probes that will bind to complementary DNA
78
FISH
fluorescent in situ hybridization and has 3 different types of probes
79
Metagenomics
DNA is isolated from an environmental sample and sequenced, metagenomic information must still be confirmed in cultured organisms
80
Microbial consortia
communities of bacteria that cannot grow without each other
81
Different methods for counting microbes
direct counts, viable counts, and turbidity measurements
82
Direct counting
counting bacterial cells and sample needs to be representative of the bacteria in the outside world
83
Viable cell counting
cells are counted on the plate that had to come from cells that are alive
84
Flow cytometry
used for viable cell counting which can be used to distinguish the cells that are dead to the one that are alive by staining
85
Turbidity measurement
uses cloudiness to see the density of the cells
86
CFU
the number of colonies counted divided by dilution and multiplied by the amount plated in millimeters and only for viable cells
87
What is the growth curve and it's 4 phases?
measure the growth of a batch culture
| lag, log/exponential, stationary, and death
88
Lag phase
when the cell synthesizes new components to replenish and adapt to new environments/conditions
89
Log phase
growth and division rate is constant and maximal
90
Stationary phase
population growth eventually ceases, it is a closed system and this phase is due to nutrient limitation, limitation of oxygen and toxic waste accumulation, survival strategies are activated
91
Death phase
number of viable cells exponentially declines
92
VBNC
populations will decrease at a constant rate and have some population of bacteria that will die at a constant rate but the plateau will have subpopulations that survive
93
The two hypotheses as to why subpopulations survive
cell are viable but not culturable so they cannot replicate, organisms are viable and not culturable since we would not notice
94
Programmed cell death
a portion of the population is pre-programmed to die and when they die they leave nutrients for the subpopulations to survive
95
Balanced growth
cellular constituents manufacture at constant rates relative to each other
96
Unbalanced growth
rates of synthesis of cell components vary relative to each other, they are not making components at the same time
97
What happens during a shift down?
take bacteria from rich media to a poor media
98
What happens during a shift up?
take bacteria from poor to rich to see what happens
99
What are 3 things we can find using the growth curve?
generation time (how long for a population to double), how quickly the growth is moving over time so number of generation per unit of time, and max population density or amount of cellular material produced by the culture
100
Doubling time
environmental factors affect it and it varies by species, it is the slope of the log phase
101
Importance of semi-log scale
the distinct phases would not be seen if it was not a semi-log graph
102
Open system
continuous culture and is replenished constantly, low nutrient concentration, mimic aquatic environments
103
Chemostat
continuous culture system, flows in fresh medium and takes out some old medium to keep culture in continuous operation, constant cell density
104
Turbidostat
continuous culture system, constituency being monitored to see the absorbent rate
105
Photocell
regulates the flow rate of media through a vessel to maintain a predetermined turbidity or cell density
106
Sterilization
all living cells, spores, and objects are killed
107
Disinfection
lower the overall microbial load and load of pathogen, not killing everything
108
Sanitization
reduction of microbial population to levels that are considered safe to public health
109
Antisepsis
destroying to inhibit microorganisms on living tissue
110
Chemotherapy
use of chemical to kill or inhibit the growth of microorganisms within living tissue
111
Cidal agents
antimicrobial agents that directly kill microorganisms
112
Static agents
inhibits the growth of microorganisms, stops replication
113
Conditions influencing the efficacy of antimicrobial agents
population size, population composition (some bacteria are easier to kill), concentration (intensity of microbial agent), contact time (cannot be killed instantly), temperature (increase temperature kills more), local environment (organic matter might lower eticassy), measuring the killing efficiency at a given temperature
114
What are physical control methods?
filtration, temperature, steam sterilization tyndallization, pasteurization, dry heat sterilization, radiation-UV, ionizing radiation
115
Filtration
method of purifying liquids for centuries
116
Ultrafiltration
requires high pressure so you have to use a vacuum to pull liquid
117
Temperature
about heating, it is a perfect way to disinfect, deproteins, RNA pulls apart lead to death
118
Freezing
ice crystal forms and kill the bacteria
119
Steam sterilization
must be carried out above 100 degrees celsius at 15 psi for about 10-15 minutes, you kill everything including endospores
120
Tyndallization
a microorganism has spores but cannot go in an autoclave and this kills spores, triggering the spores to go to their vegetative form since it is easier to kill them
121
Pasteurization
not sterilizing, this is a low temperature heating cycle, lower out microbial load
122
Dry heat sterilization
moisture, requires high temperature over long periods of time, difficult to kill spores
123
Radiation-UV
it can damage DNA causing problems with DNA replication and eventually population will die and form thymine dimers
124
Ionizing radiation
deeper and more penetrating because of the gamma rays, kill spores, and be agents of sterilizations, takes energy from gamma rays
125
Chemical control agents
disinfection, antisepsis, and sterilization
126
Disinfectants
chemicals used on non-living surfaces to kill pathogenic microbes
127
What does a good disinfectant do?
kill a wide range of microbes, should not be corrosive, should not leave a residue, should not smell too bad, should be cheap, and should be temperature stable
128
Phenolics
contains a aromatic ring structure and make their way into the cell membrane and disrupt them and denature proteins, they kill endospores, toxic
129
Aldehydes
most effective antimicrobial agents, kill endospores, sterilant, react with nucleotides and proteins
130
Alcohol
can be used as disinfectant and antiseptics but not sterilants, cannot be used as 100% concentration since it dehydrates cells
131
Iodine
skin antiseptic that can be used at high concentrations to kill spores so can be sterilant, can take protons out of things and can affect proteins
132
Chlorine
forms disinfectant, while in gas form it is a sterilant, likes to destroy bacteria in vegetative state by pulling electrons and interrupting their function
133
Heavy metals
Can kill most things except endospores, toxic, like to combine with and inactivate proteins and can precipitate proteins
134
Quaternary ammonium compounds
act as wetting agents and emulsifiers, hydrophilic portion is positive so are amphipathic and can get into warm membrane and interrupt them and can denture proteins, inactivate with soap and water
135
Sterilizing gases
they are sterilants, used to sterilize heat sensitive materials like plastic, most commonly used is ethylene oxide
136
Bacterial morphology
cocci, rod and comma shaped
137
Multicellular organization
hyphae (branching filaments of cells), mycelia (tufts of hyphae), trichomes (smooth, unbranched chain of cells)
138
Average size of cells
.5 to 5 micrometers
139
Surface/volume ratio
this constraints how big the cell can get, the more surface/volume means more beneficial, rod shaped have higher ratio
140
What is in the cytoplasm?
nucleoid, plasmid, ribosome, inclusion bodies
141
Inclusion bodies
granules of organic or inorganic material, some enclosed by single layer membrane, function is storage of nutrients, metabolic end products and building blocks
142
Ribosomes
entire ribosome - 70S, small subunit - 30S and large subunit -50S
143
Plasmids
exist and replicate independently of chromosomes, inherited stably during cell division, can be out during cell division
144
Conjugative plasmids
found in various bacteria and undergo conjugation
145
R plasmids
antibiotic resistant bacteria
146
Col plasmids
associated with E. coli and make bacterocins that can kill other bacteria
147
Virulence plasmids
make virulence factors such as toxins
148
Metabolic plasmids
make enzymes
149
Function of cytoskeleton
keeps everything in the cell, move things to correct locations, a series of internal proteins
150
FstZ
cell division
151
MamK
positioning magnetosome
152
MreB
maintains cell shape, secretes chromosomes, localizes proteins
153
CreS
induces curvature in curved rods
154
Par R
acts as a signal for Par M
155
Par M
moves copies of plasmid DNA molecules to the opposite ends of the bacterial cell
156
Plasma Membrane
composed of phospholipid bilayer, are amphipathic
157
Functions of plasma membrane
encompasses the cytoplasm, selectively permeable barrier, interacts with external environment, capturing energy, hold sensory systems
158
Peripheral membrane proteins
loosely connected to membrane
159
Integral membrane proteins
amphipathic, move laterally through membrane, carry out important functions, attached to membrane
160
Passive diffusion
molecules move from higher concentration to lower concentration, not energy dependent
161
Facilitated diffusion
high concentration to low concentration, not energy dependent, uses membrane bound specific carrier molecules
162
Active transport
energy dependent, molecules move against their concentration gradient, involves permeates (specific carrier proteins )
163
Primary active transport
uniport, ABC transporters, uses energy from ATP hydrolysis to move against their concentration gradient
164
Secondary active transport
MFS transporters, symport (2 molecules move in same direction), antiport (2 molecules move in opposite directions) couples the potential energy of ion gradients to transport
165
PTS system
group translocation, found in facultative anaerobic bacteria, not in aerobes, involved in chemotaxis
166
Siderophores
for iron uptake, secreted by the microorganisms, ferric iron is very insoluble so uptake is difficult without
167
Gram negative secretion system
two membranes with bigger periplasmic space than gram positive bacteria, active transport by hydrolyzing ATP, type 5 does not have domain
168
Sec system
secretion of unfolded proteins that first remain inside the cell
