Midterm 1 Flashcards
(374 cards)
1
Q
True or false: microbes have adapted to every known environment on earth
A
True
- many live under extreme conditions that no plant or animal can tolerate
- Antarctic ice, geothermal vents, 2 km below the Earth’s surface
2
Q
LUCA
A
Prokaryotic organism that evolved more than 3.5 billion years ago
3
Q
Where is the oldest fossil evidence of microbes found? Explain
A
Stromatolites
- Microbes form a biofilm on the surface of the water which gets covered with sand and then another biofilm surface is formed which is then covered with sand etc.
4
Q
True or false: 99% of life on earth is eukaryotic
A
False
- 99% of life on Earth is prokaryotic
5
Q
What are three applications of good microbes?
A
- Human microbiome - microorganisms living in/on us (e.g. assist in digestion, vitamin synthesis, etc.)
- Food, medicine and Industry
- fermentations yield dairy products, alcoholic products, etc
- insulin, cavvines, phage therapy
- feritlizers, industrial solvents, waste and water treatment - Global biogeochemical cycles
- carbon, nitrogen, phosphorous, etc.
6
Q
What are 4 applications of bad microbes?
A
Food, medicine and industry
- food spoilage
- illness
- corrosion
- acid mine drainage
7
Q
True or false: microbes are the leading cause of lethal diseases today
A
False; this used to be the case is the 1900s but we’ve eliminated many microbes from causing us disease.
- Antibiotic resistance can change this in the future though
8
Q
What are some applications of “ugly” microbes?
A
Severe (and antibiotic resistant) pathogens
- Viral diseases such as Lassa, ebola, HIV and SARS
- Bacterial diseases such as cholera, tuberculosis, botulism and toxic shock syndrome
- Antibiotic resistant pathogens such as MRSA and VRE
9
Q
Robert Hooke (4)
A
- Discovered cells by examining cork under his handmade microscope (dead plant cells)
- Coined the the “cell” (what he saw reminded him of honeycomb cells)
- FIRST TO OBSERVE MICROBES
- Magnification was 30X
10
Q
Antoni van Leeuwenhoek (5)
A
- Examined pond water (as well as cells from human tissues and fluid like blood and sperm)
- Total magnification was 300X
- Reported his observations of “wee animalcules” (the microorganisms in some of the fluids)
- FIRST TO OBSERVE BACTERIA
- Homunculus -> “small human” observed in sperm, thought to go to uterus for nourishment
11
Q
Louis Pasteur general contributions to science (4)
A
- Microbial metabolism: discovered many chemical reactions were the metabolic reactions of microbes
- Against spontaneous generation (swan-necked flask experiment)
- Sterilization
- Vaccines
12
Q
Describe Louis Pasteur’s contributions to MICROBIAL METABOLISM (2)
A
Alcohol fermentation reactions involve the transformation of sugars into ethanol
- Investigating vats of beet juice that were producing lactic acid instead of ethanol, he observed: healthy (ethanol-producing) vats contained yeast; spoiled (lactate-forming) vats contained bacteria -> first documented case of contamination
- Further experiments demonstrated fermentations are due to microbial metabolism, and different microbes carry out different types of fermentation
13
Q
Describe Louis Pasteur’s contributions to spontaneous generation theory (2)
A
Spontaneous generation: The idea that life can arise spontaneously from non-living matter (e.g. if you leave bread out long enough, mold will spontaneously form)
- hypothesized that microbes found on spoiled food was contamination by microbes from the environment (and that they don’t arise spontaneously)
- Developed swan-necked flask experiment to demonstrate sterile nutrient solutions would remain sterile indefinitely if microbes from the environment were prevented from entering the solution
14
Q
Swan-necked flask experiment (6 steps)
A
- Nonsterile poured into flask
- Neck of flask drawn out of flame
- Liquid sterilized by extensive heating and steam forced out of open end
- Liquid cooled slowly
- Dust and microorganisms trapped in bend due to gravity, so liquid remains sterile indefinitely.
- But if flask is tipped to get the fluid into the neck, the flask is contaminated and the liquid putrefies.
15
Q
Describe Louis Pasteur’s contributions to sterilization (2)
A
Developed mechanisms of sterilization used in research, medicine, food and production industries:
- aseptic technique (rules we follow so our work doesn’t contaminate us and we don’t contaminate our work)
- pasteurized: heating something to sterilize it
16
Q
Describe Louis Pasteur’s contributions to vaccines
A
- Developed early (crude) vaccines.
- Used attenuated (old) strains, worked on Anthrax and rabies.
- He may have taken credit for the work of others
17
Q
Robert Koch general contributions to science (2)
A
- Germ theory of disease
- Culture techniques
18
Q
Describe Robert Koch’s contributions to the germ theory of disease (2)
A
- Demonstrated the link between microbes and infectious diseases (TB, cholera, anthrax)
- Koch’s postulates (criteria for associating a microbe with a disease) were used to identify the cause for dozens of microbial infections which is still applied today in a modified form
19
Q
Koch’s 4 postulates
A
- The suspected pathogen must be present in all cases of the disease and absent from healthy animals
- The suspected pathogen must be grown in pure culture
- Cells from a pure culture of the suspected pathogen must cause disease in a healthy animal
- The suspected pathogen must be reisolated from the animal and shown to be the same as the original
20
Q
Describe Robert Koch’s contributions to culture techniques (2)
A
(Developed numerous methods for growing microorganisms in the lab and techniques for working with, and maintaining pure cultures)
- Developed multiple staining techniques (microbes are naturally hard to see under the microscope)
- Research associates Walther Hesse and Richard Petri developed a mechanism to grow microbes on solid media (Agar was suggested by his wife, after he first used potato peels then gelatin)
21
Q
Sergei Winogradsky contributions to science (3)
A
Microbial ecology:
- Demonstrated that specific bacteria are linked to specific biogeochemical transformations (nitrogen and sulfur cycles, and he developed the Winogradsky column)
- Described chemolithotrophy (oxidation of inorganic molecules for energy) and autotrophy (CO2 for carbon)
- Demonstrated microbial nitrogen fixation (N2 -> NH3) and nitrification (NH3 -> NO2 ->NO3)
22
Q
What is the Winogradsky column in general?
A
A way to culture many microorganisms at once by emanating multiple conditions of the environment in one test tube
23
Q
Martinus Beijerink contributions to science
A
Enrichment culture
- Developed multiple methods to select for organisms with specific metabolic requirements (essential to study microbial ecology and nutrient cycling, enriches the growth of specific organisms by providing an environment that promotes their growth)
- Discovered the symbiotic nitrogen-fixing bacteria (Rhizobia) in root nodules of leguminous plants (peas, beans, lentils)
- First to isolate a virus (referred to it as a “contagious living liquid” because he knew it wasn’t a bacterium but wasn’t sure what it was)
24
Q
What are the 4 ways we can study the diversity of microbes?
A
- Morphological diversity
- What they look like; what they’re made of - Metabolic diversity
- How they acquire carbon and energy - Genomic diversity
- What functions they are capable of based on the possession of certain genes - Evolutionary diversity
- Where they fit in the tree of life
25
Ferdinand Cohn contributions to science (2)
- Considered the father of bacterial taxonomy (originally organized microbes into 4 groups based on cell shape)
- Coined the term "bacteria" which literally means small rod or staff
26
What 4 groups did Ferdinand Cohn originally organize microbes into?
1. Sphaerobacteria
2. Microbacteria
3. Desmobacterium
4. Spirobacterium
27
Sphaerobacteria shape and example
Sphere-shaped
- micrococcus
28
Microbacteria shape and example
Rod-shaped
- bacterium
29
Desmobacterium shape and example
Filamentous (grow in chains that branch out)
- bacillus, vibrio
30
Spirobacterium shape and example
Coiled
- spirillum, spirochaete
31
What are 7 examples of morphological diversity in bacteria?
1. Membrane and cell wall structures
2. Motility and flagellar motion
3. Swarming (used for locomotion, doesn't use flagella)
4. Endospore formation
5. Pigmentation (seen on plates when many bacteria are present)
6. Cell arrangement (how they look under the microscope beside each other)
7. Growth under various conditions (complex media, single-carbon media)
32
How can microbial diversity be measured?
By physiological processes
33
What are two ways that metabolic diversity is measured
1. How do microbes obtain their energy?
- chemolithotrophy
- chemoorganotrophy
2. How do microbes obtain their carbon?
- heterotrophy
- autotrophy
34
Chemolithotrophy
Microbes obtain their energy from inorganic molecules (H2, H2S, Fe2+, etc)
35
Chemoorganotrophy
Microbes obtain their energy from organic molecules (sugars, proteins, etc.)
36
Heterotrophy
Microbes obtain their carbon from organic molecules
37
Autotrophy
Microbes obtain their carbon through CO2
38
Other than energy and carbon requirements, what are 4 other characteristics of metabolic diversity in microbes?
1. O2 requirements
- Aerobic, anaerobic, facultative (can grow in either condition)
2. Optimal growth conditions
- Temperature, pH, ...
3. Specific nutritional requirements:
- Metal cofactors and vitamins
4. Relationship with other organisms
- Planktonic (free-floating individual cells), symbiotic, parasitic
39
What are three ways that genomic diversity is measured in microbes?
1. Average nucleotide identity (ANI)
- Computational method of comparing two genomes
2. Identify presence of specific gene
- Presence of nitrogen fixation genes can group organisms by metabolic diversity
3. Full genome sequencing and comparison of metabolic pathways, etc.
40
True or false: The cytoplasmic membrane is semi-permeable
True
41
Hydrophobic portion of the bacterial cytoplasmic membrane
Fatty acids
42
Hydrophilic portion of the bacterial cytoplasmic membrane
Glycerol + phosphate and another functional group (e.g. sugars, ethanolamine, choline)
43
What kinds of molecules will pass through bacterial cytoplasmic membranes? Give 6 examples
Nonpolar molecules/weakly polar molecules
- e.g. H2O, ethanol, nonpolar solvents, CH4, O2, NH3
44
What kinds of molecules will not pass through bacterial cytoplasmic membranes? Give 3 examples
Large or strongly polar molecules
- e.g. ions, sugars, amino acids
45
Describe the fluidity of the bacterial cytoplasmic membrane
Has the fluidity of light oil (fluid mosaic model)
46
Describe the fatty acids in the bacterial cytoplasmic membrane
Usually 12-20 C atoms long, most C-C bonds are single but a few are double (called an unsaturation)
47
How are fatty acids in lipid membranes adapted in thermophils (in general)?
Adapted in thermophils to be more saturated (can pack better)
48
Describe the linkages of lipids to glycerol in Archaea vs. Bacteria/Eukarya
- Ether linkages (C-O-C without C=O) linkages to glycerol in membrane lipids of Archaea
- Bacteria and Eukarya have ester linkages in phospholipids
49
True or false: Archaea, Bacteria and Eukarya all have fatty acids
False; Archaea lipids lack fatty acids; have isoprenes instead (simple hydrocarbon with a methyl branch)
50
Most lipids in archaea are glycerol ____ with ______ side chains and __________ with _________ side chains, which can form _______
Most lipids in archaea are glycerol diethers (2 ethers attached to glycerol) with phytanyl C20 side chains and diglycerol tetraethers with C40 side chains, which can form lipid monolayers
51
True or false: archaeal membranes exist as only lipid monolayers
False; archaeal membranes exist as lipid monolayers, bilayers, or a mixture of both
52
What are two adaptations of thermophils seen in archaeal membranes?
1. Ether linkages are more thermostable than ester linkages
2. Archaeal lipid membranes can exist as a monolayer
53
What are 3 major functions of the cytoplasmic membrane?
1. Permeability barrier: prevents leakage and functions as a gateway for transport of nutrients into and wastes out of the cell.
2. Protein anchor (site of proteins that participate in transport, bioenergetics and chemotaxis because prokaryotes don't have any internal membrane systems so need protein anchors)
3. Energy conservation (site of generation and dissipation of the proton motive force, outer membrane + cell walls can help maintain the proton motive force)
54
What are three types of membrane proteins?
1. Embedded proteins: integral membrane proteins
2. Transmembrane proteins: extend completely across the membrane
3. Peripheral membrane proteins: loosely attached on both sides of the cell membrane
55
What are 4 major functions of membrane proteins?
1. Transport (nutrient uptake, osmotic balance, protein secretion)
2. Environmental sensing
3. Electron transport, respiration
4. Membrane and cell wall assembly
56
What are the three mechanisms of active transport?
1. Simple transport
2. Group translocation
3. ABC system
57
Describe simple transport
Transport through a transmembrane transport protein
- not the same thing as simple diffusion (which is passive transport)
- e.g. antiporters
58
Describe group translocation
Chemical modification of the transported substance (glucose) driven by phosphoenolpyruvate as soon as the solute moves into the cell
- series of proteins involved (phospho cascade)
- prevents glucose from elaving and doesn't mess up the glucose concentration gradient
59
Describe the ABC (ATP binding cassette) system
3 components:
- binding protein
- transmembrane transporter
- ATP-hydrolyzing protein that is peripheral to the transmembrane channel
60
What 3 things are cell envelopes composed of?
1. Cell membranes (1 or 2)
2. Cell wall
3. S (slime) -layers
61
What are the two main cell envelope arrangements in bacteria?
Gram negative and gram positive
62
Describe gram negative cell envelope
Cytoplasmic membrane, thin cell wall (that doesn't provide much structural support), periplasm, outer membrane (which replaces the role of a thicker cell wall)
63
Describe gram positive cell envelope
Cytoplasmic membrane and thick cell wall (no outer membrane)
64
What is the thick cell wall in gram-positive bacteria made of?
Peptidoglycan and teichoic acid/lipoteichoic acid (teichoic acid covalently attached to phospholipids)
65
True or false: only gram + cells have peptidoglycan in their cell walls
False; both cell types have peptidoglycan in their cell walls
66
What is the periplasm and what is it important for?
The space found between the outer and inner cell membranes of gram-negative cells
- lots of metabolism is carried out here because the cell pushes enzymes into this space which cannot diffuse out
67
Gram-negative cells are (pink/purple) when stained and gram-positive cells are (pink/purple) when stained
pink, purple
68
Most bacteria are gram (negative/positive)
- Explain why
Negative
- because 2 membranes provides a huge selective advantage to bacteria
69
True or false: most archaea are gram negative
False; archaea aren't assigned gram + or - because their cell membranes/walls are much different
70
Describe the 4 steps for a gram stain procedure
1. Flood the heat-fixed smear of bacteria with crystal violet dye: all cells become purple since crystal violet diffuses into both cell types
2. Add iodine solution, which complexes with crystal violet to keep crystal violet attached to the cell wall.
3. Add ethanol. In gram - cells, ethanol strips away the membrane and rips the peptidoglycan apart which allows the crystal violet to diffuse out. So gram + cells are purple and gram - cells are colorless
4. Do counter-stain with safranin: red dye helps us see the cells because after the crystal violet rushes out, it's hard to see the cells. So gram + cells are purple and gram - cells are red
71
What are the two main functions of the cell wall?
1. Maintains cell shape and rigidity
2. Need to withstand osmotic/turgor pressure to prevent cell lysis
72
What do bacterial cell walls contain that isn't found in archaea or eukarya?
Peptidoglycan
73
Peptidoglycan
A rigid polysaccharide layer that provides strength
74
Subunit of peptidoglycan
Glycan tetrapeptide
75
What does the glycan tetrapeptide contain? (2)
1. Sugar backbone (alternating modified glucose N-Acetylglucosamine - NAG and N-Acetylmuramic acid- NAM) joined by β-1,4 linkages (in an alternating fashion)
2. 4 amino acids (that vary between species)
76
What does the tetrapeptide in glycan tetrapeptide allow for?
Attaching several glycan chains
77
Which modified glucose moiety does the tetrapeptide attach to in glycan tetrapeptide? How does it bind?
N-Acetylmuramic acid (NAM)
- The tetrapeptide is bound through its amino group to a carboxyl group on the NAM.
78
How is peptidoglycan organized around the cell? (in both gram + and gram - cells)
- Peptidoglycan strands run parallel around cell circumference
- Cross-linked by covalent peptide bonds
79
How are the peptidoglycan crosslinks arranged in gram-negative cells?
Crosslinks between diaminopimelic acid (DAP) and D-alanine carboxyl on adjacent glycan strands
80
How are the peptidoglycan crosslinks arranged in gram-positive cells?
Crosslinks often contain peptide interbridges (e.g. five glycines in Staphylococcus aureus between amino acids of adjacent glycan tetrapeptides)
81
Gram + bacteria have up to __ layers of petidoglycan while gram - bacteria have up to __ layers of peptidoglycan
20, 3
82
Gram-positive cell walls contain up to __% peptidoglycan, 15 or more layers thick
90
83
True or false: gram negative cell walls often only have a single layer of peptidoglycan
True
84
Describe teichoic acid (4)
- Acidic, negatively charged
- Found in certain gram +
- Strongly antigenic
- Covalently bound to the peptidoglycan
85
Lipoteichoic acids
Teichoic acids also covalently to membrane lipids
86
What are five functions of teichoic acid?
1. Maintain porosity of cell wall (keeps layers separate)
2. Anchors cell wall to cell membrane
3. Helps maintain cell shape
4. Captures essential cations (e.g. Ca2+, Mg2+)
5. Can be a reservoir of phosphate
87
What are the three features of the G- cell envelope
1. Periplasm
2. Porins
3. Lipopolysaccharide
88
Porins
Channels for movement of hydrophilic low-molecular-weight substances through the outer membrane
89
True or false: phospholipids are present in the outer half of the outer membrane in the G- cell envelope
False; lipopolysaccharides (polysaccharides covalently bound to lipids) are present instead of phospholipids in the outer half of the outer membrane
90
Function of lipopolysaccharide in G- cell envelope
Facilitates surface recognition, important virulence factors, and add strength
91
True or false: the cell wall is stronger than the lipopolysaccharide layer
False; the LPS is stronger
92
What 3 components make up the structure of the bacterial lipopolysaccharide?
1. O-specific polysaccharide/O-antigen
2. Core polysaccharide
3. Lipid A
93
LPS lipid A general structure
Can have multiple fatty acid tails (not necessarily two like in regular phospholipids)
94
LPS core polysaccharide general structure
Types of sugars is species-specific (differs between species)
95
LPS O-specific polysaccharide general structure
Highly variable between species
- Also called "O-antigen" -> what our immune system recognizes
96
____ is an endotoxin. What does this mean?
Lipid A; it can cause endotoxic shock
Endotoxin: anything that is a permanent part of a cell that can cause a toxic response in other cells.
- When your cells start dying, lipid A is released to bloodstream -> toxic effect
97
What is found in archaeal cell walls instead of peptidoglycan?
Pseudomurein
98
Pseudomurein
- Like peptidoglycan, but NAG binds to N-Acetyltalosaminuronic acid (TAL) through β- 1,3 bond
- Subunits of pseudomurein are held together by peptide cross-bridges
99
Bactoprenol (undecaprenol diphosphate)
Lipid made of hydrocarbon and two phosphates that moves peptidoglycan subunits into the periplasm
100
Lipid II
Bactoprenol + peptidoglycan precursor
101
What are the 4 steps of peptidoglycan synthesis?
1. Autolysins break the β 1-4 bond between between NAM and NAG sugars in the peptidoglycan chains (happens quickly so osmotic pressure doesn't make the cell explode)
2. Assembly of lipid II (ABC transporter protein), which is transported across the membrane via flippase
3. Transglycosylases insert the precursors into the broken peptidoglycan chain and reforms surgar bonds between old and new parts of the strand.
4. Transpeptidation reforms peptide cross-links between peptidoglycan subunits
102
What antibiotic(s) inhibits transglycosylases involved in peptidoglycan synthesis?
Vancomycin
103
What antibiotic(s) inhibits transpeptidases involved in peptidoglycan synthesis?
Penicillin and vancomycin
104
What type of protein is flippase?
ABC transporter protein
105
What is peptidoglycan synthesis crucial for?
Bacterial growth
106
What are two agents that destroy peptidoglycan? How do they work?
1. Lysozyme (found in tears and egg whites)
- Hydrolyzes peptidoglycan by breaking the β 1-4 bond between NAm and NAG sugars
2. Antibiotics
- e.g. Vancomycin, Beta-lactam antibiotics (penicillin, etc.)
- Inhibit formation and/or cross-linking of the glycan strands
- Attack the enzymes involved in peptidoglycan synthesis
107
How do bacteria acquire antibiotic resistance?
Bacteria quickly figure out how to outsmart antibiotics via enzymatic degradation (e.g. Beta-lactamases) and membrane alterations
108
What 5 Fts proteins interact to form the divisome?
1. FtsZ
2. ZipA
3. Ftsl
4. FtsK
5. FtsA
109
FtsZ
Fts (filamentous temperature-sensitive) protein that forms a ring around center of cell; it has been found to have structural homology to tubulin in eukaryotes
110
ZipA
Anchor that connects FtsZ ring to cytoplasmic membrane
111
FtsI
Peptidoglycan biosynthesis protein
112
FtsK
Assists in chromosome separation
113
FtsA
An ATPase
114
MinCD
Inhibits the formation of the FtsZ ring
115
MinE
Oscillates from pole to pole, sweeping MinCD aside
- clears MinCD from the middle of the cell and towards the poles which allows Ftsz to form in middle of cell
116
When the cell becomes very long, there is (great/little) MinCD in the middle of the cell
Little
117
What shape do bacteria become when no cytoskeletal proteins are found?
Cocci (sphere)
- so default is cocci
118
Crescentin
Shape-determining protein found in curved cells
- Organizes into filaments ~10 nm wide that localize on concave face of the curved cells
119
MreB
Major shape-determining factor in prokaryotes
- Forms a simple cytoskeleton with patchlike filaments around inside of cell just below cytoplasmic membrane in bacteria and some Archaea
- Recruits other proteins for cell wall growth to group into a specific patters
- Pushes cocci out into a rod (so not found in coccus-shaped bacteria)
120
True or false: MreB is found in cocci bacteria
False
121
S-layers are found in...
Archaea
122
Describe the S-layers (5)
- Common cell wall component among Archaea (and some bacteria)
- Consist of a protein or glycoprotein monolayer
- Act as structural support (rigid), molecular sieves (semi-permeable), and to form a pseudo-periplasmic space (like in a G- cell)
- Attachment to surfaces and biofilm formation
- Protection from grazing/immune systems/antibiotics/Protection from desiccation (filled with water)
123
S (slime) layer can also be called what 3 other things in different phyla?
Capsule, exopolysaccharide, glycocalyx
124
True or false: the slime layer makes bacteria and some archaea sticky and may be larger than the bacteria itself
True
125
Peritrichous flagella
Multiple flagella
126
Monotrichous flagella
Only one flagella
127
Lophotrichous flagella
Multiple flagella coming out one side of the bacteria
128
Fimbriae
Filamentous protein structures 2-10 nm wide
- Fibriae enable organisms to stick to surfaces or form pellicles (thin sheets of cells on a liquid surface)
129
Pili
Pili are typically longer, thicker, and fewer (1 or a few) found per cell than fibriae
130
Conjugative pili
Facilitate genetic exchange between cells (conjugation)
- F-pillus
131
Type IV pili
Adhere to host tissues and support twitching motility
132
What are inclusion bodies in general?
Generalized name that we give to strange things we find inside prokaryotes
133
What are the 4 classes of inclusion bodies?
1. Carbon/energy storage polymers
2. Polyphosphate granules
3. Sulfur globules
4. Carbonate minerals
134
What are the two types of carbon/energy storage polymers (inclusion bodies)?
1. PHA (polyhydroxyallkanoates): a family of lipids that include PHB
(poly-beta-hydroxybutyric acid)
- If cells run out of carbon, they can consume PHA molecules
2. Glycogen
135
Describe polyphosphate granule inclusion bodies
Inorganic phosphate storage
- polymers of phosphate groups
136
Describe sulfur globule inclusion bodies
Elemental sulfur in periplasm can be oxidized to sulfate (SO4 2-)
137
What organisms are sulfur globules found in?
Lithotrophic organisms (obtain energy from inorganic compounds)
138
Describe carbonate mineral inclusion bodies
Biomineralization (the process by which living organisms create minerals, called biominerals, within their bodies) of barium, strontium, and magnesium
- Function is unknown, but probably just a source of carbonate for the cell.
139
What are two protein-bound compartments in prokaryotes?
1. Chlorosomes
2. Carboxysomes
140
What are chlorosomes?
Light antennae, they allow the bacteria to grow at low light intensities
141
What are carboxysomes?
Concentrated areas for the Calvin cycle to happen (loaded up with enzymes required)
- Some obligate chemolithotrophs and photolithotrophs
142
What is the key enzyme found in the carboxysomes that is involved in CO2 fixation?
RubisCO-
143
What are gas vesicles?
Buoyancy regulators in some planktonic bacteria
- Help in aquatic bacteria, especially those that photosynthesize as gas vesicles change their density and determine their depth
144
What are magnetosomes?
Giant collections of magnetic iron oxides that allow the cell to undergo magnetotaxis: migration along magnetic field lines
- Bacteria probably use the magnetic field to determine up vs. down
- Magnetosomes are arranged in chains
145
Describe endospores
Highly differentiated cells resistant to heat, harsh chemicals, and radiation
- "Dormant" stage of bacterial life cycle
- Ideal for dispersal via wind, water, or animal gut
- Only formed when growth ceases due to lack of an essential nutrient such as carbon or nitrogen (harsh environmental conditions)
- can remain dormant for years but convert rapidly back to being a vegetative cell
146
Endospores are only present in what type of bacteria?
Gram-positive
147
"Internal" membranes are found in what three types of bacteria?
Phototrophic, nitrifying and methanotrophic bacteria
148
Describe "internal" membranes in bacteria
- Membranes are usually connected to the cytoplasmic membrane so they are "invaginations" rather than separate compartments
- Key enzymes for these bacteria are membrane-bound, so more invaginations = more surface area = more enzyme
149
Nitrification
Lithotrophic oxidation of ammonia to nitrate, usually occurs as two separate reactions by different groups of bacteria
- Many species have internal membrane systems that house key enzymes in nitrification
Reaction: NH3 -> NH2OH -> NO2 -> NO3
150
Ammonia oxidizers (ammonia monooxygenase)
Involved in nitrification
- e.g. Nitrosococcus
- ammonia monooxygenase oxidizes NH3 to NH2OH
151
Nitrite oxidizers
Involved in nitrification
- e.g. Nitrobacter
- nitrite oxidase: oxidizes NO2 (nitrite) to NO3 (nitrate)
152
During nitrification, the membrane that houses enzymes required for NH3 -> NO2- (ammonia monooxygenase) are located near the (middle/periphery) of the bacteria
Middle
153
During nitrification, the membrane that houses enzymes required for NO2- -> NO3- (nitrite oxidase) are located near the (middle/periphery) of the bacteria
Periphery
154
Some planctomycetes have other internal membrane structures such as... (2)
Annamoxosome (carries out a special form of nitrogen fixation) and a nucleoid
155
Habitat definition and their constraints (in general)
Parts of an ecosystem suited to a particular group of populations
- Constrained by physical limits of temperature, water activity, pH
156
True or false: prokaryotes have much broader ecosystem ranges than eukaryotes
True
- but not every species can inhabit every habitat, even if microbes are found pretty much everywhere
157
What are 6 RESOURCES that provide a constraint on habitat composition?
1. Carbon (organic, CO2)
2. Nitrogen (organic, inorganic)
3. Macronutrients (S, P, K, Mg) -> nutrients that organisms need in large quantities
4. Micronutrients (Fe, Mn, Co, Cu, Zn, Mn, Ni)
5. O2 and other electron acceptors (prokaryotes don't only use O2)
6. Inorganic electron donors (H2, H2S, Fe2+, NH4+, NO2-
158
What are 6 CONDITIONS that provide a constraint on habitat composition?
1. Temperature
2. Water potential: dry ->moist -> wet
3. pH
4. O2: oxic -> microoxic -> anoxic
5. Light
6. Osmotic conditions: freshwater -> marine -> hypersaline
159
Species richness definition
The total number of different species present
160
Species abundance definition
The population size of each species in an ecosystem
161
What is a guild?
Metabolically-related microbial popoulations
- Perform key steps in biogeochemical cycles.
- e.g. oxygenic phototrophs vs. aerobes vs. denitrifying bacteria
162
Microenvironment definition
The small part of a local environment encountered by a given species (very localized)
163
Describe the physiochemical conditions and resources in a microenvironment
Subject to rapid change, both spatially and temporally
- Resources in natural environments are highly variable, and many microbes in nature face a feast-or-famine existence
- Competition and cooperation occur between microbes in natural systems
164
True or false: growth rates of microbes in nature are usually the same as maximum growth rates defined in the lab
False; growth rates of microbes in nature are usually well below maximum growth rates defined in the lab
165
What 4 things are soils composed of? What are their relative proportions? Which are considered to be limiting factors?
1. Inorganic material (~40% of soil volume)
2. Dead organic matter (~5%)
3. Air and water (~50%)
4. Living organisms
Limiting factors: energy source (organic matter) and inorganic nutrient availability
166
The availability of ___ often limits microbial activity in surface soils
Water
167
Rhizosphere
The area around plant roots where plants secrete sugars and other compounds, is rich in organic matter and microbial life
168
What are the three main layers of soil from top to bottom?
1. Organic matter
2. Nutrient-rich soil
3. Organisms using inorganic substances
169
As you get deeper into soil, what happens to oxygen content and nutrients?
Aerobic environment (oxic) becomes anaerobic (anoxic) and organic matter becomes inorganic
170
True or false: There are diverse microenvironments in soils and microbial diversity is very high (even in single grains of soil)
True
171
What are the steps for identifying bacteria in an environmental sample using SSU rRNA sequences?
1. Isoalte DNA from environmental sample (not pure culture) and amplify the 16S ribosomal gene by PCR. Instead of the SSU gene from a singel bacterium, you get a mixture of SSU genes from all bacteria in your sample.
2. Run agarose gel; check for correct size.
3. Simultaneously sequence thousands of your SSU genes with next-generation sequencing technologies
4. Align sequences; generate tree
172
What is an OTU (operational taxonomic unit)? What does molecular sampling indicate about OTUs in most soils?
Usually defined as a 16S rRNA gene sequence that differs from all other sequences by >3% (presumed to represent a species). Would be the same OTU if differences <3%.
- Molecular sampling indicates that there are 1000s to 100,000s of different microbial species (OTUs) in most soils
173
What are the 4 major components (in order of greatest to least) of soil bacterial and archaeal diversity?
1. Proteobacteria
2. Acidobacteria
3. Bacteroidetes (sphingobacteria, flavobacetria, and other bacteroidetes)
4. Actinobacteria
174
True or false: Nearly all 16S rRNA genes recovered from environments like soil do match cultured species at >97% identity (or 98.7%)
False; nearly all 16S rRNA genes recovered from environments like soil do not match cultured species at >97% identity (or 98.7%)
- There are about 13,000 cultured, named species but an estimated 1 million to 1 trillion uncultured species (OTUs that won't grow in the lab).
175
Describe the great plate count anomaly
<1% of bacteria seen under a microscope is actually able to be cultured
176
Due to the size of the oceans, the microbial activities taking place in them are...
Major factors in Earth's carbon balance
177
________ typically contain higher microbial numbers than the open ocean because of ______
Near-shore marine waters, higher nutrient levels.
178
Describe the distribution of chlorophyll between coastlines and oceans
Greater concentration of chlorophyll on coast, but as you go deeper into the water, less chlorophyll is seen
179
What are the 4 major components of coastal ocean bacterial and archaeal diversity?
1. Proteobacteria
2. Marinimicrobia
3. Bacteroidetes
4. Actinobacteria
180
What is most of the primary productivity in the open oceans due to?
Photosynthesis by cyanobacteria
181
Describe Prochlorococcus (2)
Photosynthetic cyanobacteria in ocean
- >40% of the biomass of marine phototrophs
- ~50% of the net primary production of the ocean (net primary production of the ocean is ~25% that of the entire Earth
182
Pelagic bacteria is also known as...
Open ocean bacteria
183
What is the most abundant marine ORGANOHETEROTROPH?
"Pelagibacter"
- in " because organism hasn't been officially speciated yet
184
What is an oligotroph?
An organism that grows best at very low nutrient concentrations (evolved to eat very little; nutrient rich conditions are toxic to these cells).
185
True or false: "Pelagibacter" was long known from molecular DNA studies to be the most abundant bacterium in the ocean, but it took decades to finally grow a strain, and it has still not been validated as a true species
True
186
What does pelagibacter contain?
Proteorhodopsin, a form of rhodopsin that allows cells to use light energy to drive ATP synthesis (but still has heterotrophic enzymes, can't be sustained with just autotrophy)
187
What was the largest marine oil spill ever, and its consequences on the environment?
Deepwater Horizon oil spill in the Gulf of Mexico
- Oil released as a plume at great depths
- Bloom of hydrocarbon-degrading microorganisms, as they have previously adapted to using oil (petroleum) as a fuel source because the Gulf of Mexico has a lot of oil seepage
- Early growth of hydrocarbon-degrading bacteria reduced the environmental impact.
188
What do organisms that inhabit the deep sea deal with? What are these organisms called?
Called extremophiles
Have to deal with:
- Low temperature
- High pressure
- Low nutrient levels
- Absence of light energy (many lithotrophs)
189
What is a biofilm?
Assemblages of bacterial cells adhered to a surface and enclosed in an adhesive matrix excreted by the cells (matrix = mixture of polysaccharides)
190
Microbes can be planktonic (floating freely) or attached to a surface. Which do most microbes prefer and why?
Most microbes like to be attached to a surface because it's easier for them to get nutrients going to them instead of having to go find them.
191
How is biofilm formation initiated?
Initiated by attachment of a cell to a surface followed by the expression of biofilm-specific genes (then attached bacteria start to grow and divide)
- The genes encode proteins that initiate matrix formation
192
Quorum sensing definition/function, and what the major quorum sensing molecules are
Sensing and responding to the population density, which is critical in the development and maintenance of a biofilm.
- Allows the cells in the biofilm to have an idea of how abundant other species are.
Major quorum sensing molecules are acylated homoserine lactones
193
What are 3 reasons why bacteria form biofilms?
1. Self-defense
- Biofilms resist phagocytosis by immune system cells, and penetration of toxins (e.g. antibiotics)
2. Trap nutrients for microbial growth and help prevent detachment of cells in a flowing system
3. Allow bacterial cells to live in close association with one another - facilitates cross-feeding and symbiosis
194
What is a big problem with medical implants like catheters and artificial joints?
The formation of biofilms (since they're mostly antibiotic-resistant and very few effective atibiofilm agents are available because they're hard to penetrate)
Biofilms have been implicated in several medical and dental conditions:
- including periodontal disease, cystic fibrosis, tuberculosis, etc.
195
Describe the impact of biofilm in industrial settings
Biofilms can slow the flow of liquids through pipelines and accelerate corrosion because biofilm loves to form in areas with water present (e.g. oil pipelines - damages are in the billions of dollars per year)
196
What are microbial mats and where do they usually form?
Very thick biofilms (often seen in hot springs)
- Built by massive collections of phototrophic and/or chemolithotrophic bacteria
- Phototrophic mats have existed for over 3.5 billion years (stromatolites)
- Often occur in systems with low predation/grazing, e.g. extreme ecosystems.
197
-philes vs -tolerant
-philes: Organisms that can grow in different ranges of environmental parameters
-tolerant: Organisms that can survive in different ranges of environmental parameters
198
Minimum cardinal temperature
The lowest temperature at which an organism can survive
- Membrane gelling; transport processes so slow that growth cannot occur
199
Optimum cardinal temperature
All functions are at peak capacity
- enzymatic reactions occurring at maximal possible rate
200
Maximum cardinal temperature
Sharp decrease
- Protein denaturation; collapse of the cytoplasmic membrane; thermal lysis
201
Temperature optimum of Psychrophile
4 degrees C
- Not a crash down at the maximum temp because the proteins aren't denaturing, just getting too warm to work properly
202
Temperature optimum of Mesophile
39 degrees C
203
Temperature optimum of Thermophile
60 degrees C
204
Temperature optimum of hyperthermophile (found in hot springs and hydrothermal vents)
88 degrees C and 106 degrees C
205
Most organisms can survive in ranges of ___ degrees C
30
206
What are thermophilic habitats typically made of?
Compost, decaying organic matter
207
Thermophilic habitats are located in the...
Deep biosphere (30 degrees C increase for every 1 km in depth)
- Geothermal systems, like hot springs, mud pools, undersea vents
208
Hyperthermophiles live in what temperature?
>80 degrees C
209
What are the "champions" of hyperthermophiles?
Archaea
- But some bacteria are still hyperthermophiles
210
No eukarya grow above ___ degrees C
62
211
True or false: different processes have different maxima
True
- e.g. photosynthesis stops at 73 degrees C
- Enzymes limit metabolic activity of organisms
212
What types of organisms are found in hydrothermal vents (2)
Thermophiles and hyperthermophiles
213
What type of prokaryotes utilize inorganic materials from the vents?
Chemolithotrophic prokaryotes
214
What types of organisms are associated (but not actually found in) deep-sea hydrothermal vents?
Thriving animal and microbial communities
215
What are the main primary producers in deep-sea ecosystems?
Bacteria
216
Relationships between animals and microbes in deep-sea environments?
Any animals are eating the microbes or have symbiotic microbes
217
What are 3 problems that microbial life deal with at high temperatures?
1. Proteins denature
2. DNA/RNA denature
3. Membranes too fluid
218
How do microbes deal with denaturing proteins at high temperatures?
Form stronger bonds to stabilize proteins (e.g. DNA polymerase bonds differ in thermophiles)
219
How do microbes deal with denaturing DNA/RNA at high temperatures? (2)
Increased GC content (increases RNA stability, reverse gyrase (positive supercoiling of DNA)
220
How do microbes deal with membranes being too fluid at high temperatures?
Decrease membrane fluidity (via tetra-ethers)
221
What are 5 features of thermophilic enzymes and proteins that provide thermal stability?
1. Critical amino acid substitutions in a few locations provide more heat-tolerant folds
2. Increased number of ionic bonds between basic and acidic amino acids resists unfolding in the aqueous cytoplasm
3. Highly hydrophobic interiors
4. Production of solutes (e.g. di-inositol phosphate, diglycerol phosphate) helps stabilize proteins
5. Smaller, more spherical proteins with less quaternary structure
222
What are 3 problems that microbes have to deal with at low temperatures?
1. Proteins too rigid and slow reaction rates.
2. Membranes too viscous
3. DNA/RNA too rigid
223
What is a solution to microbe proteins being too rigid and slow reaction rates at low temperatures?
Reduced amino acid interactions that stabilize tertiary structures
224
What is a solution to microbe membranes being too viscous at low temperatures?
Increased membrane fluidity
225
What is a solution to microbe DNA/RNA being too rigid at low temperatures?
Decreased GC content
226
Each microbe has a pH range of ______ pH units within which growth is possible
2-3
227
Neutrophiles
Organisms that grow optimally within a pH range of 5.5-7.9
- e.g. humans
228
Alkaliphiles
Organisms that grow best at high pH (>8)
229
Acidophiles
Organisms that grow best at low pH (<5.5)
230
What is the problem with acidophiles and alkaliphiles
The cytoplasm must be near neutral pH, therefore the cell membrane must therefore be very impermeable to protons
231
True or false: it's difficult to maintain a proper proton motive force in both extreme acidic and alkaline conditions
True
232
How is a neutral cytoplasmic pH maintained in acidophiles?
Lots of H+ is able to rush in through ATPase from electron transport chain. This makes lots of ATP, which can then be used to power proton pumps, pumping H+ out of the cell
233
How is a neutral cytoplasmic pH maintained in alkaliphiles?
No proton motive force is maintained for ATPase (H+ diffuses in environment quickly), so Na+/H+ antiporter pumps H+ in and Na+ out. H+ is pumped "with concentration gradient" technically because the H+ builds up in the periplasm, enough to go down an antiporter. Na+ is then pumped through the ATPase instead of H+, creating ATP and powering H+ pumps pumping H+ into the cell.
234
Halophiles definition and 3 examples
Love salt
- Bacteria, Archaea, Eukarya
235
Xerophiles definition and example
Love dry conditions
- Fungi
236
Osmophiles definition and example
Love osmotic stress (in principle any osmotic stress, but usually applied to organisms adapted to high sugar concentrations)
- yeasts
237
Non-halophile %NaCl optimum
0
238
Halophile %NaCl optimum
1-15%
239
Extreme halophile %NaCl optimum
>15% optimum
240
What is water activity? What are lower values caused by?
Water activity is a measure of vapour pressure.
Lower values are caused by dryness and solutes
241
What does aw(in)
Water moves into the cell
- As water moves in, the increased pressure in the cell increases the water activity inside, eventually balancing out the solute effect
- This isn't the end of the world due to cell walls
242
What does aw(in)>aw(out) mean in terms of water movement? What effect does this have on the cell?
Water flows out of the cell
- is lethal
243
What are 2 strategies used by halophiles to avoid osmotic stress? What organisms use each?
1. "Salt in" strategy: accumulate KCl (need salt-adapted enzymes)
- mostly Archaea, few bacteria
2. "Compatible solutes" strategy: accumulates organic solutes (not ions, but still draws some water in)
- Bacteria and Eukarya
244
True or false: compatible solutes damage enzymes
False; compatible solutes, unlike salts, do not damage enzymes
245
How do Halobacterium make ATP?
Can make ATP via a very simple system using Bacteriorhodopsin
- Bacteriorhodopsin absorbs photons to produce proton motive force, which then results in producing ATP
- first example of a non-photosynthetic proton-driven proton pump
246
Aerobe definition
Require O2 for respiration
247
Microaerophiles
Require O2 but at low [] (atmospheric concentrations of O2 are toxic)
- In thioglycolate broth, grow just below the surface
248
Facultative anaerobes/aerobes
Will respire if O2 is available but can survive without it
249
Aerotolerant anaerobes
Do not use O2 but can tolerate it
250
Obligate anaerobes
Don't use O2 nor can they tolerate it
251
Thioglycolate broth
- What do the different layers mean?
A complex medium that distinguishes microbes based on oxygen requirements
- Resazurin reacts with oxygen, so oxygen can penetrate only a few mm from the top of the tube
Colourless layer: No O2, is in reduced form: anoxic layer
Red colour: O2 present, is in oxidized for: oxic zone
252
True or false: halophiles are found in salt water environments (not other hypersaline environments)
False; halophiles are found in hypersaline environments, which are way saltier than seawater
253
True or false: all bacteria are motile
False; not all bacteria are motile
254
What are 4 types of motility in bacteria?
1. Gas vesicles that allow vertical movement
2. Swimming via flagellar rotation
3. Gliding motility
4. Twitching motility using pili
255
What two types of bacteria are flagella found on?
Rod-shaped or curved bacteria
256
Flagella size in length and diameter
15-20 µm in length, 15-20 nm in diameter
257
Flagella follow a _____ shape
Helical
258
What protein makes up flagella?
Flagellin
259
Flagella is similar to what other structure?
ATP synthase
260
L and P rings in flagella?
Sleeves in the peptidoglycan and outer membrane
- L = LPS, P = peptidoglycan
261
C ring in flagella
Embedded in cell membrane
- C = cytoplasm
262
Mot proteins in flagella
Stator (doesn't move but is part of the catalytic part of the protein)
263
MS ring + rod in flagella
Rotor (part that spins)
264
True or false: flagella use proton motive force to move, and they span both cell membranes in G- bacteria
True
265
True or false: if a cell has the ability for motility, it will turn on its motility genes
False; it will not always turn on its motility genes
266
What are the the 2 steps for flagella biosynthesis?
1. Basal structures formed first
2. Flagellin moves up through hollow core and attaches to terminal end via self assembly (an exporter, the filament grows from the tip)
267
Describe counterclockwise flagellar rotation in peritrichous bacteria
Flagella form a trailing bundle (looks like a lofotrichous looking structure), and the bacterium will swim straight forwards
268
What is it called when bacteria swims straight forwards?
Run
269
Describe clockwise flagellar rotation
Flagella fly apart and the bacterium tumbles RANDOMLY (like a pause in swimming)
270
True or false: bacteria usually don't go anywhere
True
271
Bacteria like at a very (low/high) Reynolds number, meaning that the friction of water is (small/large) compared to momentum. As soon as flagellated bacterium ceases driving its flagellum, it...
Low, Large, comes to a dead stop
272
True or false: bacteria are at the mercy of currents, unless they can stay attached to a surface
True
273
True or false: there is an advantage to some bacteria in being able to move along a surface
True
274
Describe twitching motility
Bacteria is attached to surface, and extends pilus forward to attach to surface. Cell then jerks to the new position
275
Describe gliding motility
Bacteria is attached to surface, and "track" protein rotates along bacterium, but proteins are always attached to the surface so the bacteria moves forward
276
Positive vs. negative phototaxis
Positive: movement towards certain wavelengths of light
Negative: movement away from certain wavelengths of light
277
Positive vs. negative aerotaxis
Positive: movement towards O2 or a gradient of O2
Negative: Movement away from O2 or a gradient of O2
278
Thermotaxis
Response to temperature or a temperature gradient
279
pH taxis
Movement towards or away from acid/alkaline environments or gradients
280
Magnetotaxis
Directed movement along the geomagnetic lines of force which allows magnetotactic bacteria to seek microaerophilic environments necessary for growth
281
Chemotaxis
Directed movement in response to certain chemicals known as chemoeffeectors
282
What are the two ways that an external signal is transmitted to a target?
Either directly to a target, or it is sense and a signal transmitted to regulatory machinery (signal transduction)
283
True or false: most signal transduction systems are two-component regulatory systems
True
284
What two components make up two-component regulatory systems? (and extra component)
1. Sensor kinase (usually in the cytoplasmic membrane): detects environmental signal and autophosphorylates. Transmits signal via phospharylation of a....
2. Response regulator (in cytoplasm): usually a DNA-binding protein that regulates transcription
* also has a feedback loop which terminates the signal
285
What are 2 examples of compatible solutes?
Glycine betaine and ectoine
286
True or false: Halobacteria live in high salt concentration and use a lot of compatible solutes
True
287
Why is oxygen toxic in general?
Due to presence of reactive oxygen species (ROS)
- These strip electrons off of anything around them (e.g. proteins)
288
What are three examples of ROS?
1. Superoxide anion (O2-)
2. Hydrogen peroxide (H2O2)
3. Hydroxyl radical (OH.)
289
Catalase function
Reforms H2O2 into water and O2
290
Peroxidase function
Reduces H2O2 into water and NAD+
291
Superoxide dismutase
Combines superoxide anion to form H2O2 and O2
292
What extra enzyme(s) do organisms that use superoxide dismutase and superoxide reductase need?
Catalase or peroxidase to get rid of H2O2
293
Superoxide reductase
Gets rid of superoxide anion by reducing it
294
Describe the steps behind the control of gene expression by a two-component regulatory system, using a sensor kinase (4 steps)
1. Sensor kinase is bound by environmental signal and His is phosphorylated by ATP
2. Response regulator (mobile protein in cytoplasm) steals phosphate from His to reset sensor kinase
3. Response regulator acts as a transcription regulator (either activator or repressor)
4. Response regulator is dephosphorylated by ADP to form ATP, and cycle restarts upon binding of environmental signal
295
True or false: bacteria cannot detect chemical concentration gradients
True
296
Bacteria respond to (temporal/spatial) differences in chemical concentration
Temporal
- The length of the runs changes depending on whether conditions are becoming better or worse
- This temporal sensing allows them to adjust the frequency of their "run and tumble" behaviour, based on whether conditions are improving
297
Describe biased random walk in general
used in chemotaxis, allows directed movement. Inn this process, the length of the runs changes depending on whether conditions are becoming better or worse
298
Describe how bacteria swim towards attractants, starting from the binding of attractants to MCP receptors (3 steps)
1. The binding of the attractant to the MCP shuts down the MCP pathway.
2. Shutting down MCP pathway results in bacteria swimming in a straight line (flagella moves in counterclockwise manner)
3. As the bacteria swims towards attractant, more attractant binds and the bacteria will continue swimming in the same direction
299
Describe how bacteria swim towards repellants, starting from the binding of repellants to MCP receptors including signal termination (9 steps)
1. The binding of the repellant to the MCP turns on the MCP pathway
2. CheW will help the sensor kinase CheA become phosphorylated
3. CheA phosphorylates the response regulator CheY and sometimes also phosphorylates CheB
4. CheY goes to the flagellar motor, attaches, and causes the rotation to switch from counterclockwise to clockwise. This causes the bacteria to tumble.
5. The bacteria will then move into a random direction.
6. If the bacteria starts moving away from the repellent, less repellent will bind to the MCP and the MCP system will not turn on anymore -> bacteria continues swimming away from repellant
7. CheZ removes the phosphate from CheY to terminate the tumble
8. CheB that was previously phosphorylated dephosphorylates MCP to further inactivate the MCP pathway to ensure that CheY doesn't just get phosphorylated again
9. MCPs have a gradually increasing amount of methylation due to CheR, making them increasingly more likely to signal a tumble
300
Describe what happens to the MCP pathway when a bacterium swims away from an attractant including termination (6 steps)
1. Less attractant binds to the MCP receptors, turning on the pathway.
2. CheW helps the sensor kinase CheA to get phosphorylated
3. CheA then phosphorylates the response regulator CheY, which goes to the flagellar motor and causes clockwise rotation (and phos. CheB)
4. The bacteria then runs randomly
5. CheZ removes the phosphate from CheY to terminate the tumble
6. CheB that was previously phosphorylated dephosphorylates MCP to further inactivate the MCP pathway to ensure that CheY doesn't just get phosphorylated again
301
Function of CheR in the mechanism of chemotaxis?
Continuously methylates the MCP to reactivate the pathway
302
What protein is the off switch for CheY-P?
CheZ
303
What protein is the on switch for MCPs? What protein is the off switch?
ON: CheR (by methylation)
OFF: CheB
304
Describe how the chemotaxis pathway resets (4 steps)
1. CheB-P demethylates MCPs, causing them to become less active and stop phosphorylating CheY
2. CheZ resets CheY-P to the inactive CheY state
3. Run recommences
4. CheB-P gradually returns to the inactive CheB state.
305
What 4 things are in a bacterial growth medium?
1. Energy source (organotrophs, lithotrophs, phototrophs)
2. Carbon source (autotrophs, heterotrophs)
3. Macronutrients (nutrients required in large amounts)
4. Micronutrients (nutrients required in trace amounts)
306
What are the 4 classes of culture media?
1. Defined media
2. Complex media
3. Selective medium
4. Differential medium
307
What is defined media?
Exact chemical composition is known
308
What is complex media?
Composed of digests of microbial, animal, or plant products (e.g. yeast and meat extracts)
309
What is a selective medium?
Contains compounds that selectively inhibit growth of some microbes but not others
310
What is a differential medium?
Distinguishes organisms with specific metabolic capabilities
- Contains an indicator, usually a dye
311
Describe the typical growth curve for a bacterial population
1. Lag phase: cells getting ready to divide, perhaps not expressing the genes requried for growth in the flask so they aren't exponentially dividing yet
2. Exponential: bacteria divide very quickly
3. Stationary: Waste starts to accumulate and nutrients become limiting; cells are dividing and dying at equal rates
4. Decline
312
Generation time meaning for bacteria in a flask
All of the bacteria in the flask divide every __ hours
313
Exponential growth equation
Nt=N0 * 2^n
- Nt is cells at time t
- N0 is cells at start
- n= number of generations
314
Generation time formula
n=t/g
- n= number of generations
- t= the amount of time you let the culture grow
- g= the generation time (h), the amount of time required for a population of cells to double
315
Describe coulter counters
A known volume of microbial suspension forced through a small aperture. When a cell moves through the aperture, it disrupts an electric current (increases resistance)
- Instances of current disruption are counted
316
Describe flow cytometry
Is similar to coulter counters except it uses a laser beam that is disrupted rather than an electrical current
317
What is the main problem associated with coulter counters/flow cytometry?
You don't know if what's passing through the sensor is actually a cell, or if its alive or dead
318
Describe the direct microscopic counting procedure using the Petroff-Hausser counting chamber
After loading your sample onto a slide with grids, you count the cells in several grids then average it out. You then calculate the number of cells per mL of sample by using various conversion factors
319
What are 6 limitations of microscopic counting chambers?
1. Cannot distinguish between live and dead cells without special stains
2. Small cells can be overlooked
3. Precision is difficult to achieve
4. Cell suspensions of low density (<10^6 cells/mL) is hard to count
5. Motile cells need to be immobilized
6. Debris in sample can be mistaken for cells
320
Describe viable cell counts methods
Measurement of a living, reproducing population
1. Spread-plate method: sample is pipetted onto surface of agar plate, spread evenly over surface of agar using sterile glass spreader, and typical spread-plate results show colonies that can be converted into cell count based on dilution factor
2. Pour-plate method: same thing as above just sample is pipetted into sterile plate which is mixed with a sterile medium
321
How to convert viable count plate into cell count/mL of sample
Colony plate count x Dilution factor
322
Describe the most probable number (MPN) method of counting cells, and when it is used
The tubes are incubated and checked for turbidity (more cloudy = more cells). The most dilute tube with growth has the reciprocal dilution factor of the stock culture.
- Used to estimate population sizes in wastewater, food and other industrial settings. Valuable when cells do not grow well on solid media, cell numbers are low, time is short
323
How to figure out concentration of stock solution through serial dilution MPN analysis
Take most dilute tube with growth present and subtract 1 from dilution factor
324
Describe optical density (turbidity) counting method
Quick, easy and efficient indirect counting method
Procedure:
1. Light shines through prism, then through sample
2. Unscattered light reaches photocell which is detected by spectrophotometer (spits out OD
- As cell number increases, optical density increases
325
Actual cell number x optical density curves differ from the direct theoretical value at higher densities. Why does this occur?
Caused by deflection of light from cell, that hits another cell and bounces back to the plate to be detected.
- Gives us an underestimate of how many cells are actually present
326
Describe a batch culture
Growth in a closed system, MEDIUM NOT REPLENISHED (see typical bacterial growth curve with lag, exponential, etc)
- Growth conditions are constantly changing; it is impossible to control growth parameters
327
Describe a continuous culture
An open-system microbial culture of fixed volume (ensures death stage doesn't occur)
- continuously replenishing medium
328
Describe the chemostat and what 2 factors are controlled in one
Most common type of continuous culture device
- Both growth rate and population density of culture can be controlled independently and simultaneously
- Can be maintained at constant growth rates for long periods of time
- Fresh medium dripping in at a constant rate, and at the same time, waste media is leaving, usually at the same rate
329
Dilution rate in chemostat and what it controls
The rate at which fresh medium is pumped in and spent medium is pumped out
- Controls what phase of the growth cycle the bacteria are in (growth rate)
330
What happens if dilution rate is relatively high (but not too high) in chemostat?
Cells are kept in exponential phase, because a high concentration of a limiting nutrient is flowing in
331
How do we control the number of cells in a chemostat culture?
By changing the amount of a limiting nutrient
332
How is the growth rate in a chemostat controlled?
By dilution rate
333
How is the population density (cell number/ml) controlled in a chemostat?
Controlled by concentration of a limiting nutrient
334
What is steady state in the chemostat?
Cells grow at the same rate that they are removed from the chemostat
- Bacterial biomass remains relatively high at steady state and limiting nutrient concentration remains low
335
What happens to specific growth rate of bacteria, bacterial biomass and the limiting nutrient concentration within a chemostat during the washout stage?
Washout occurs when dilution rate is too fast.
1. Bacterial biomass plumets
2. Specific growth rate plateaus
3. Limiting nutrient skyrockets
336
Nutrient concentrations only alter growth at (lower/higher) nutrient concentrations
Lower
337
What are five uses of a chemostat?
1. Fermentations (production of large amounts of cell mass)
2. Physiological studies
- Used to determine maximum growth rate
3. Useful tool because scientist can control growth rate and population density independently - and obtain a steady cell supply
4. Tends to simulate natural conditions better than batch culture
5. Ecological studies into competition, predation
338
True or false: the nutrient concentration in a chemostat doesn't affect the growth rate of the bacteria at all
False; at low concentrations, the nutrient concentration affects the growth rate but after a certain concentration, it doesn't impact the growth rate as it increases.
339
Which organisms contain peptidoglycan? Which don't?
Bacterial cell walls contain peptidoglycan but archaeal and eukaryotic cells don't
340
Where are methyl-accepting chemotaxis proteins (MCPs) typically located in bacteria?
At the poles of the cells
341
What happens when the dilution rate in a chemostat is faster than the growth rate?
Washout occurs and biomass decreases
342
What is an example of an environment where it would be best to isolate alkaliphilic bacteria that use sodium motive force?
Soda (salt) lakes
343
True or false: microbial life existed for billions of years before plant and animal life
True
344
Describe pelagibacter
The most abundant marine organoheterotroph, and oligotroph
345
What are 3 reasons why rRNA is preferred over other nucleotide sequences for identifying bacteria?
1. They are functionally constant (have the same function in all species)
2. They are rarely transferred from one species to another
3. They are universally distributed (All living organisms, including bacteria, possess rRNA because it is essential for protein synthesis)
346
_____ molecules are partially responsible for the ____ charge of the gram-positive bacterial cell surface
Teichoic acids, negative
347
What type of energy-yielding metabolism is only found in prokaryotes?
Chemolithotrophy
348
When is carrier-mediated transport necessary? (3)
1. When diffusion will not allow adequate amounts of a substance to enter the cell
2. Movement into the cell is against a concentration gradient
3. The level of nutrients in nature is very low
349
The tetraether molecule within the membrane structure of the _____ yields a lipid _____
Archaea, monolayer
350
What is a major difference between cells in a biofilm and planktonic cells?
Cells in a biofilm have a greater tolerance for antimicrobials
351
Although common in the past, today microbial mats develop ONLY in aquatic environments where...
Conditions restrict grazing and competition
352
Archaea and bacteria are unified in lacking ______ which Eukarya contain, such as mitochondria
Nuclei and membrane-enclosed organelles
353
What is the hook in flagella?
Where the filament attaches to the base of the flagellum
354
True or false: flagellar rotation generates ATP
False
355
Superoxide dismutase and catalase work together to convert superoxide into...
Water and oxygen
356
What type of organism would not contain superoxide dismutase or catalase?
Obligate anaerobe
357
What is an assumption of the viable plate count method?
Each colony arises from a single cell
358
What are four direct methods of measuring bacterial growth?
1. Flow methods: coulter counter/flow cytometry
2. Microscopic counts: counting chambers
3. Viable plate counts
4. MPN
359
Optical density (turbidity) is a (direct/indirect) bacterial counting method
Indirect
360
Where in the cell are sulfur granules found?
Periplasm
361
What are three examples of gram + bacteria?
Firmicutes, actinobacteria and some chloroflexi
362
Porins are found in the (inner/outer) membrane of gram (positive/negative) cells
Outer, negative
363
Who discovered the symbiotic nitrogen-fixing bacteria (Rhizobia) in root nodules of leguminous plants?
Martinus Beijerinck
364
Who discovered nitrogen fixation and nitrification?
Sergei Winogradsky
365
Who described chemolithotrophy and autotrophy?
Sergei Winogradsky
366
What organisms are carboxysomes found in?
Obligate chemolithotrophs and photolithotrophs
367
Psychrophile optimum temp range
<15 degrees C
368
Mesophile optimum temp range
15-45 degrees C
369
Thermophile optimum temp range
45-80 degrees C
370
True or false: capsules/slime layers protect against thermal stress
False; they protect against desiccation but not thermal stress
371
True or false: the outer membrane in gram-negative bacteria acts as a highly selective permeability
False; the CYTOPLASMIC membrane is the highly selective permeability barrier of the cell
372
A halotolerant facultative anaerobe would grow best in what type of environment?
Oxygenated non-saline
373
Explain the significance of bacteriorhodopsin
It allows halophilic bacteria to be phototrophic without being photosynthetic. It uses light energy to generate PMF
374
What protein(s) does CheA phosphorylate?
CheY AND CheB
