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Soil Microbiology > Lecture 3 - Exam 1 > Flashcards

Lecture 3 - Exam 1 Flashcards

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Biology 101 flashcards
1
Q

What are the two types of cell metabolism?

A

Anabolism: microbes take nutrients from the environment and they undergo biosynthesis. Autotrophs and heterotrophs undergo anabolism. Autotrophs use inorganic carbon sources and heterotrophs use organic carbon sources.
Catabolism: Energy production (energy source is chemicals and light).

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2
Q

What are the classes of organisms based on their energy source?

A

Phototrophs and chemotrophs (contain chemolithotrophs and chemoorganotrophs)

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3
Q

What is the difference between chemolithotrophs and chemoorganotrophs?

A

Chemolithotrophs use inorganic compounds as energy source (S, H2S, NH4+, NO2, and FE2+).
Chemoorganotrophs use organic compounds as energy sources.

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4
Q

What are the three different chemolithotrophs?

A

Sulfur-oxidizing bacteria, nitrifying bacteria (use ammonium -> ammonium oxidizers produce more energy or nitrite -> nitrite oxidizers as energy source), and iron-oxidizing bacteria.

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5
Q

The three types of chemolithotrophs all have what in common?

A

Oxidation-reduction reactions are being used.

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6
Q

What is oxidation?
What is reduction?

A

electron loss (removal of electron)
electron gain (addition of electron)

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7
Q

What are electron donors?
What are electron acceptors?

A

Donors: lose e-, become oxidized, are reductants
Acceptors: receive e-, become reduced, are oxidants

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8
Q

Electron donors and acceptors form:

A

Redox pairs. Ex: Fe3+/Fe2+ (we write oxidized form first)

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9
Q

What is the charge of sulfur is H2SO4?

A

6
2(+1) + S + 4(-2) = 0
solve for S

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10
Q

What are reduction potentials?

A

The tendency of a substance to donate or accept electrons is expressed as the reduction potential (E0’) of the substance.

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11
Q

How are half reactions written?

A

Oxidized form + e- = reduced form

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12
Q

There is a ________ correlation between energy gain and difference in reduction potential in redox pairs.

A

Positive.
The greater the difference in E0’ between the two redox pairs, the greater the energy available from the reaction.

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13
Q

What are the electron carriers?

A

Intermediates for electron transfer.
They are NAD+/NADH, NADP+/NADPH, FAD/FADH2 (these are all redox pairs too).

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14
Q

What are the high energy compounds where much of the energy that is generated is stored in?

A

ATP, acetyl-CoA, and phosphoenolpyruvate (PEP)

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15
Q

How are ATPs generated? (3 different ways)

A

Substrate-level phosphorylation, oxidative (electron transport) phosphorylation, and photophosphorylation.

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16
Q

What are the four different soil organisms that are classified based on body size?

A

Microflora (to describe microorganisms), microfauna (<200um), mesofauna, and macrofauna (the last three are useful when classifying larger organisms, not when we study small organisms)

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17
Q

What type of organisms has the highest biomass?
What is the general trend for body size and the number of microbes in the soil?

A

Fungi have the highest biomass.
As body size increases, the number of microbes in the soil (per gram) decreases.

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18
Q

What type of microbe is the most numerous in the soil?

A

Prokaryotes (Bacteria and Archaea)

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19
Q

For the longest time we thought __________ was the largest bacteria, but now we know ________ is larger.

A
  1. Thiomargarita namibiensis
  2. Thiomargarita magnifica
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20
Q

What are the three shapes of bacteria we find in the soil?

A

Coccus (spherical), rods (rod-shaped), and spirillum (spiral shaped)

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21
Q

What are filamentous bacteria?

A

Bacteria that are connected in chains, or filaments.

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22
Q

What is the most common shape of bacteria in the soil?

A

Coccoid rods (short rods)

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23
Q

What are pleomorphic bacteria?

A

Some bacteria can have more than one shape. They can alter their morphology.

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24
Q

What is true about microbes in the soil versus their counterparts (like aquatic microbes)?

A

They are smaller in the soil (shape and size).

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25
Q

Gram positive stains are what color? How about gram negative?

A

Gram positive: purple
Gram negative: pink/reddish

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26
Q

What is the step in the gram staining process where gram negative will not retain the purple color? What is the step where it gains its pink color?

A

Decolorization step.
Counter stain (safranin)

27
Q

What are the steps in gram staining?

A

Fixation (no color), add crystal violet, add iodine, decolorization, and add counter stain (safranin)

28
Q

What is the difference between G+ and G- cell walls?

A

G+: primarily PG (90%), contain teichoic acids, use peptide bridge as cross linkage.
G-: Multicomponents in cell wall (thin layer PG, outer membrane (LPS & protein), and periplasm), no teichoic acids, direct cross linkage between DAP & D-alanine

29
Q

Peptidoglycan is only found in?

A

Bacteria

30
Q

What gives Gram positive their negative charge?

A

Teichoic acids (b/c they have negative charge)

31
Q

What gives G- their negative charge?

A

Comes from outermembrane

32
Q

Some bacteria are gram variable… What does that look like? (on the graph)

A

Start as G+ coccoid rods, become G+ filament (briefly), then grow rapidly and filaments turn into G- rods, and then at the end will become G+ coccoid rod.
Change in terms of their shape and cell wall structure.

33
Q

Describe acid-fast bacteria.

A

Generally considered G+, don’t stain well.

34
Q

Describe Mycoplasmas.

A

Obligate parasites. Have no cell wall, will not retain dye.

35
Q

What kind of bacteria do we think we have more of in the soil? G+ or G-?

A

G- because it is more ecologically expensive & more carbon and nitrogen intensive to form a big, thick PG layer.

36
Q

How many Bacteria and Archaea are there in one gram of soil?

A

10^9-10^10

37
Q

What is the general size range of bacteria?

A

Diameter: 0.5 um
Length: 1-2um

38
Q

Describe spores.

A

They can tolerate heat, dryness, acidity. They are formed by organisms like Bacillus and Clostridium under environmental stress. Once environmental conditions increase, they will germinate and begin to grow again. It is a survival structure.

39
Q

When we talk about bacterial growth, are we referred to size or numbers?

A

Referring to the number of bacteria in a population.

40
Q

Describe binary fission.

A

The formation of two daughter cells from one parent cell. Occurs at an individual level.
Involves generation and generation time.
Generation: One parent cell becoming two daughter cells.
Generation time: Time it takes for one cell to become two. 2^n … E. coli have generation time of 20 minutes
0 min : 1 cell
20 min : 2 cell
40 min : 4 cells
etc.

41
Q

What are the four phases of bacterial growth?

A

Lag phase, exponential (log) phase, stationary phase, death phase

42
Q

What is soil bacterial motility like?

A

Soil bacteria do not move much in the soil, even though they have the genetic capability to. They do not produce flagella in the soil. They stay where the food is (interface between soil solids and soil solution). They don’t move by themselves, but under physical forces (like when it rains), they can move to places like lower in the soil profile.

43
Q

Flagella vs. Pili

A

Flagella: long filaments that rotate and allow them to move.
Pili: short filaments responsible for attachment and gliding motility.

44
Q

What are the two reasons that bacteria do not move on their own in the soil?

A

Nutrients at the interface and energy conservation.

45
Q

What is Reynolds number?

A

the ratio of inertial force to viscous force.
R = inertia force / viscous force

46
Q

Describe myxobacteria.

A

Use gliding motility. Live on rotten leaves and animal waste. When nutrients run out, they aggregate and produce spores. They become fruiting bodies and once the environment gets better, the myxospores germinate.

47
Q

What are the names of some common soil bacteria?

A

Bacillus, Arthrobacter, Pseudomonas, Agrobacterium, Clostridium, Alcaligenes

48
Q

Actinobacteria vs Fungi.

A

Fungi: have nucleus, 80S ribosomes, have larger filaments, have chitin in cell wall, produce spores, produce antibiotics, degradation of recalcitrant compounds.
Actinobacteria: no nucleus, 70S ribosomes, have smaller filaments, peptidoglycan in cell wall, produce spores, produce antibiotics, degradation of recalcitrant compounds, and is the source of earthy smell in soil - Geosmins.

49
Q

Example of antibiotics?

A

Tetracycline, Tylosin, Streptomycin sulfate salt, Kanamycin

50
Q

What are the major targets for antibacterial action?

A

Target cell wall biosynthesis, protein biosynthesis, and DNA replication and repair.

51
Q

Antibiotics with different targets trigger a common killing mechanism. What is it?

A

Triggers the TCA cycle and eventually hydroxyl radicals cause damage that leads to cell death.

52
Q

How do actinobacteria adapt to the antibiotics they produce?

A

Temporal separation of antibiotic production from growth (when they are growing, they don’t produce antibiotics… they produce antibiotics during stationary phase when there is less nutrient rich media for growth) and development of resistance mechanisms:
-modification of the target molecules (can modify ribosome attachment site so antibiotics won’t bind there)
-antibiotic is not actually active until it is excreted
-exported actively (pumped out)
-become impermeable to the antibiotic and not take it up at all after it has exported it out.

53
Q

What are the two ways the Macrolides adapt to the antibiotics they produce?

A

Modify ribosome surface, methylate amino functional group, and then antibiotics can’t bind. They also do not have active antibiotics until it is excreted.

54
Q

What is the ecological significance of antibiotics?

A

Actinobacteria will produce antibiotics to eliminate their competitor, although we are not completely sure.

55
Q

Describe antibiotic resistance.

A

If not used at high concentrations and not completed to the fullest, then antibiotic resistance arises in bacteria. Antibiotics were also used in feed for animals, but that has been recently banned, but was contributing to the resistance issue. Genes in bacteria carry antibiotic resistance, and plasmids spread easily. That’s why it is such a big deal.

56
Q

Describe Cyanobacteria.

A

Unicellular or filamentous. They are oxygenic phototrophs and use light as their energy source. Their electron donor is water. Use chlorophyll a and contain lamellae which is a membrane structure. They also have a cell wall comprised of a thin layer of PG and a sheath (which helps individual cells attach to others to form colonies), and their storage carbon is a starch-like substance or oil. Some can fix nitrogen via heterocysts.

57
Q

What do lichens do?

A

A composite organism made up of algae and fungi, that have a symbiotic relationship. Lichens provide shelter for cyanobacteria and are known for “eating rocks,” or weathering them. They also help play a role in soil formation.

58
Q

Are archaea genetically similar to bacteria?

A

NO! They are only morphologically similar.

59
Q

Archaea have what instead of peptidoglycan in their cell wall?

A

Pseudopeptidogylcan

60
Q

What kind of linkages are made between sugars in the pseudopeptidoglycan?

A

Occurs in archaea, so these linkages are B(1,3) and are lysozyme-insensitive. This is unlike bacteria that have B(1,4) linkages and are sensitive to lysozyme.

61
Q

With regard to the membrane phospholipids, what are different between an archaea and bacteria membrane phospholipid structure?

A

Archaea: have branched isoprene chains that are resistance to degradation (due to their branchedness), ether linkages, and L-glycerol.
Bacteria: have unbranched fatty acids, ester linkages, and D-glycerol.

62
Q

Archaeal organisms have different cell wall compositions, and membrane lipids than bacteria do. What else is different?

A

Different structural proteins in chromosomes, more complex RNA polymerases, different shape of 70S ribosomes (more rigid ribosomes for hyperthermophiles), use different pathways for glucose catabolism, and have different sensitivity to antibiotics.

63
Q

David Bergey contributed what to science?

A

The classification of prokaryotes. He had two manuals and the second edition of the second manual was based on genetic relatedness. He listed the 7 categories:
Domain, phylum, class, order, family, genus, and species (most detailed).

Soil Microbiology (10 decks)

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