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From Flashcardlet > Micro Test 3 > Flashcards

Micro Test 3 Flashcards

1
Q

What is a methanogen?

A

They generate and release CH4 (methane)

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2
Q

What type of respiration do methanogens use?

A

Anaerobic respiration

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3
Q

What TEA does a methanogen use?

A

CO2

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4
Q

What is the chemical reaction for methanogenesis?

A

CO2 + 4H2 –> CH4 + 2H2O

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5
Q

What electron donor do methanogens use?

A

H2 (great e- donor because it is high up on the electron tower)

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6
Q

Is CH4 a product or a TEA for methanogens?

A

Product!

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7
Q

What domain do methanogens belong in?

A

Subset of archaea

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8
Q

Where do some anaerobic reactions occur?

A

Deep oceans, wetland sediments, landfills, rumerns of cows, flooded soil (anywhere without O2)

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9
Q

What could CH4 be used for?

A

Could be used as a fuel source

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10
Q

How have the habitats for methanogens increased in recent years?

A

There are more environments where CH4 is created because humans have created more landfills, rice patties, and animals GI tracts

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11
Q

How does O2 affect methanogens?

A

O2 is toxic to methanogens

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12
Q

Why would a microbe need to respire other organic molecules besides glucose?

A

Because they usually don’t have a ready supply of glucose in their environment

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13
Q

What are some forms of energy sources other than glucose?

A

Carbohydrates, lipids, proteins and amino acids, organic pollutants (petroleum), aromatic hydrocarbons

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14
Q

What are four examples of glucose polymers?

A

Cellulose, starch, chitin, glycogen

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15
Q

How does an organism break down large carbs into monomers? Where do these large carbs come from?

A

Large carbs from plants and animals are degrade by specific enzymes (ex. cellulase, chitinase)

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16
Q

What kinds of monosaccharides besides glucose would enter glycolysis?

A

Galactose, fructose, mannose

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17
Q

In general, what kind of enzymes break down di and polysaccharides?

A

Hydrolases and phosphorylases

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18
Q

Are lipids highly oxidized or reduced?

A

Reduced

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19
Q

What kind of enzyme breaks down fatty acids? Phospholipids?

A

Lipase, phospholipase

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20
Q

What are fats broken down into? Where do the products go?

A

Break down into fatty acids and glycerol.
Fatty acids go through beta oxidation and convert to acetyl CoA, which enters the Krebs cycle.
Glycerol enters glycolysis

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21
Q

What is beta oxidation?

A

Fatty acids are degraded into several 2 Carbon subunits

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22
Q

What happens to the 2 Carbon subunits after the fatty acids are degraded?

A

The 2 Carbon subunits are converted to acetyl coA and it enters the Krebs cycle

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23
Q

What does it mean to have a bigger and longer fatty acid?

A

The more acetyl CoA can be produced and the more H+ can go to NADH and FADH2 to the Krebs cycle

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24
Q

How are fatty acids converted into 2 Carbon subunits?

A

Beta oxidation breaks the H bonds in between the carbons

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25
Q

What kind of enzyme degrades proteins?

A

Proteases

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26
Q

What are proteins broken down into?

A

Amino acids

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27
Q

What bonds are broken when a protein is degraded?

A

Peptide bonds

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28
Q

What is deamination?

A

The removal of an amino molecule

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29
Q

What happens to a phenol red broth when a protein is deaminated?

A

The pH of the broth increases and the color turns hot pink

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30
Q

What happens to a phenol red broth when a sugar is fermented?

A

The pH of the broth decreases and the color turns yellow

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31
Q

What is peptone?

A

A protein digest, a mix of amino acids

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32
Q

What domains exhibit chemolithotrophy?

A

Only bacteria and archaea - no eukaryotes!

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33
Q

What is the electron donor for a chemolithotroph?

A

An inorganic chemical

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34
Q

What is the typical TEA of a chemolithotroph?

A

O2

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35
Q

What process does a chemolithotroph use to synthesize ATP?

A

Oxidative phosphorylation

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36
Q

Does a chemolithotroph yield more or less ATP than a chemoorganotroph?

A

Less, that is why they use O2 as a TEA because it is a great TEA that can yield the most ATP they can possibly make

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37
Q

Why can’t a chemolithotroph use substrate level phosphorylation?

A

Because SLP takes the phosphate from an organic molecule - chemolithotrophs can only use inorganic substrates

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38
Q

What is the typical carbon source for a chemolithotroph?

A

CO2

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39
Q

What is a lithotroph?

A

It uses inorganic compounds as its initial electron donor for respiration

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40
Q

What is the best electron donor?

A

H2

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41
Q

What is a common electron donor for nitrification?

A

NH4 (ammonia) NO2 (nitrite)

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42
Q

What is the chemical equation for nitrification?

A

2 step process NH4–>NO2–>NO3

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43
Q

What is the waste product of nitrification?

A

NO3 nitrate

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44
Q

What is the initial electron donor for sulfur oxidation?

A

H2S hydrogen sulfate

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45
Q

What is the initial electron donor for iron oxidation?

A

Fe+2 ferrous iron

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46
Q

What is the TEA for iron oxidation?

A

Can only use O2

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47
Q

Is iron a good or bad initial electron donor?

A

Terrible, it is very low on the electron tower

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48
Q

Why is nitrification iportant?

A

Because NH4 is usually a pollutant

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49
Q

Where is NH4 typically found?

A

In fertilizers - because plants need nitrogen

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50
Q

What happens when humans use more fertilizer than needed?

A

The excess NH4 washes off into ground water and coastal environments, causing algae to grow in aquatic environments (algae can produce toxin and deprive the environment of oxygen)

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51
Q

Why are nitrifying organisms beneficial to humans?

A

Because when we over fertilize the system the organisms can remove the excess NH4

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52
Q

How are nitrifiers used in water treatment plants?

A

The nitrifiers remove ammonia from the waste water before releasing the water from the treatment plant

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53
Q

Is fermentation an/aerobic?

A

Anaerobic, it doesn’t need oxygen but can still occur in the presence of oxygen

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54
Q

Why do cells ferment?

A

To make ATP

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55
Q

How is fermentation different from respiration?

A

No ETC no PMF

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56
Q

How is ATP made during fermentation?

A

Substrate level phosphorylation

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57
Q

How much ATP is produced with fermentation?

A

Only a little

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58
Q

How does an organism compensate for the fact that fermentation produces a small amount of ATP?

A

It ferments a lot

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59
Q

Is there one process of fermentation?

A

No many pathways exist

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60
Q

What is the electron donor of fermentation?

A

An organic chemical

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61
Q

What happens to NADH during respiration?

A

NADH is regenerated by giving its electron to the ETC

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62
Q

What happens to NADH during fermentation that is different from respiration?

A

NADH is regenerated by giving its electron to pyruvate which is then reduced into lactic acid

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63
Q

Why does NADH need to be regenerated?

A

So that glycolysis can continue

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64
Q

What might NADH donate its electron to if not pyruvate?

A

Something downstream of pyruvate like acytelaldehyde

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65
Q

What are two typical waste products of fermentation?

A

Acids and gases

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66
Q

What are two types of fermentation pathways?

A

Lactic acid fermentation and ethanol fermentation

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67
Q

What is the waste product of lactic acid fermentation?

A

Lactic acid

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68
Q

What is the waste product of ethanol fermentation?

A

Ethanol and CO2

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69
Q

What happens to the waste products of fermentation?

A

They are always excreted

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70
Q

What happens to pyruvate during the lactic acid fermentation pathway?

A

NADH is oxidized to NAD and lactic acid is produced

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71
Q

What happens to pyruvate during the ethanol fermentation pathway?

A

Pyruvate is converted to CO2 and acetylaldehyde, and NADH is oxidized to NAD to form ethanol

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72
Q

What types of foods are made from propionic acid?

A

Swiss cheese

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73
Q

What types of foods are made from lactic acid?

A

Yogurt, soy sauce, cheddar cheese

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74
Q

What types of foods are made from acetic acid?

A

Vinegar

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75
Q

What types of foods are made from ethanol?

A

Beer

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76
Q

What are the two general essential elements of life?

A

Macronutrients and micronutrients

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77
Q

What are macronutrients (definition and examples)?

A

Nutrients required in large quantities - CHNOPS, Mg, Ca, K

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78
Q

What are micronutrients (definition and examples)?

A

Aka trace elements, required in very small quantities, often supplied in tap water - Co, Mn, Ni, Zn, Mo, Cu

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79
Q

How can you get trace elements into your media?

A

By mixing it with tap water

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80
Q

What are the essential elements of life used for?

A

They are nutrients needed to build cell structures to grow, eventually leading to doubling in size and division

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81
Q

How do you need to be careful when making media relating to nutrients for the organism?

A

You need to make sure that the microbe has the nutrients it needs in a form it can handle

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82
Q

What eight things does all cellular life require for growth and maintenance?

A
  1. Organic carbon
  2. Energy source
  3. Nitrogen source
  4. Phosphorus
  5. Sulfur
  6. Other nutrients (Mg, Ca, Fe, K)
  7. Micronutrients (Co, Mn, Ni, Zn, Mo, Cu)
  8. Growth factors
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83
Q

What are the two types of carbon sources?

A

Autotrophic versus heterotrophic

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84
Q

What are the three types of energy sources?

A

Photo vs chemoorgano vs chemolithotroph

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85
Q

What is nitrogen used for?

A

To synthesize proteins, ATP, peptidoglycan, and nucleic acids

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86
Q

What are some examples of nitrogen sources?

A

Inorganic NO3, NH3, N2, organic amino acids, urea

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87
Q

What is nitrogen assimilation?

A

The nitrogen taken into the cell is incorporated into cellular material

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88
Q

Why do different organisms need different forms of nitrogen?

A

Because they have different transporters to bring in nitrogen from the environment

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89
Q

How much of our air is nitrogen?

A

78%

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90
Q

What domains are nitrogen fixers?

A

Prokaryotes, never eukaryotes

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91
Q

What is nitrogen fixation?

A

Reducing nitrogen

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92
Q

What is the key enzyme of nitrogen fixation?

A

Nitrogenase

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93
Q

What does a nitrogen fixer do?

A

It converts inert N2 into a form of nitrogen that the organism can use

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94
Q

What is the cost and benefit of being a nitrogen fixer?

A

There is a huge competitive advantage in the environment but it costs a lot of ATP to do so

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95
Q

What would a nitrogen fixer do if there was already a lot of NH3 in its environment?

A

It wouldn’t fix any nitrogen until NH3 levels where low because it spends too much ATP doing so

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96
Q

What is an example of a nitrogen fixing bacteria?

A

Rhizobium

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97
Q

Where does Rhizobium reside?

A

It can detect chemicals released by leguminous plants and infects their roots

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98
Q

How is the Rhizobium in a mutualistic relationship with the legumes?

A

Its infection stimulates the plant root cells to form nodules

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99
Q

What is mutualistic symbiosis?

A

The organisms can live without each other but do better together

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100
Q

How does the Rhizobium infect the roots of legumes?

A

The root hair curls around the cell and engulfs it. The cell then divides and forms an infection thread into the plant and a symbiosome forms

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101
Q

What is a symbiosome?

A

A little nitrogen fixing factory inside the plant

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102
Q

How do the Rhizobium and the legume benefit each other?

A

The plant doesn’t produce nitrogenase, so the symbiosome fixes nitrogen for the plant. In return, the bacteria gets the sugars and O2 from the plants and has no competition or predators from the environment

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103
Q

What essential elements require sulfur?

A

Cysteine, methionine, and vitamins

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104
Q

What are the inorganic sources of sulfur?

A

Sulfate (SO$) and H2S

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105
Q

What are the organic sources of sulfur?

A

Cysteine, methionine

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106
Q

What is sulfur assimilation?

A

Sulfur taken into the cell is incorporated into cellular material

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107
Q

What is phosphorus required for the synthesis of?

A

Phosphate for nucleotides (DNA and ATP) and phospholipids

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108
Q

What are some sources of phosphorus?

A

PO4 (phosphate), organic P

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109
Q

What are growth factors?

A

Organic compounds that are essential materials that the cell cannot synthesize on its own

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110
Q

What kinds of cells need a lot of growth factors?

A

Fastidious cells

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111
Q

What are some examples of growth factors?

A
  1. Vitamins (for coenzymes)
  2. Some amino acids (essential a.a. for humans)
  3. Purines and pyrimidines
  4. Heme
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112
Q

What is an example of a cell that doesn’t need any growth factors?

A

E. coli

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113
Q

What three things do you need to be sure the media has to grow your organism?

A

Electron, carbon, and nitrogen source

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114
Q

What is selective media?

A

It favors the growth of some microorganisms and inhibits the growth of others

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115
Q

What is an example of selective media? What is it selective for?

A

Mannitol salt agar is selective for salt loving microbes

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116
Q

What is differential media?

A

It distinguishes microbes based on their traits

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117
Q

What is an example of differential media? What is it differential for?

A

Blood agar is differential for hemolytic versus nonhemolytic bacteria

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118
Q

What is defined media?

A

The exact chemical composition is known and should not vary between batches

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119
Q

What type of microbes grow in defined media?

A

Fastidious

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120
Q

What is undefined media? What is another name for it?

A

Complex media is when the exact chemical composition is not known and it varies between batches

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121
Q

What elements does complex media contain?

A

Extracts (animal, plant, yeast) and protein digests

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122
Q

What are some examples of protein digests?

A

Peptone, casein, tryptone

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123
Q

What is a protein digest?

A

A mixture of pieces of amino acids

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124
Q

How do nutrients move along a gradient when no ATP is required?

A

Down the gradient from High to Low concentrations

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125
Q

What are two transport processes where no ATP is required?

A

Passive and facilitated diffusion

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126
Q

What is passive diffusion?

A

The nutrients cross directly across the bilayer

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127
Q

What is facilitated diffusion?

A

Involves a transport protein - a permease embedded in the cell membrane with a pore where the nutrient passes

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128
Q

How do nutrients move along a gradient when ATP is required?

A

Up the gradient from areas of Low to High concentration

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129
Q

What are two transport processes that require ATP?

A

Active transport and Group translocation

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130
Q

What is the most common form of active transport?

A

ABC transport systems

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131
Q

What domains use ABC transporters?

A

All three

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132
Q

What domains use group translocation?

A

Prokaryotes

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133
Q

What transport process is specific for eukaryotes and why?

A

Endo and exocytosis. Prokaryotes cannot perform these processes because their rigid cell wall does not form vesicles

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134
Q

What influences whether a molecule will be diffused by passive or facilitative?

A

Size and charge

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135
Q

What types of molecules can use passive diffusion?

A

Small, uncharged, hydrophobic, nonpolar

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136
Q

How do nutrients flow on their gradient during passive diffusion?

A

Down the gradient

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137
Q

What types of molecules can use faciliated diffusion?

A

Large, charged, hydrophilic, polar

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138
Q

How do nutrients flow on their gradient during facilitated diffusion?

A

Down the gradient

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139
Q

Why do polar molecules need faciliated diffusion?

A

Because as the molecule moves through the phobic lipids it gets stuck

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140
Q

What structure passes molecules in facilitated diffusion?

A

Permease transporters

141
Q

Why can nonpolar molecules pass freely through the membrane?

A

Because as the molecule goes through the phobic middle lipid it can move freely and not get stuch

142
Q

Can water diffuse passively?

A

Yes but it passes faster with facilitation by an aquaporin

143
Q

What kinds of molecules have the lowest membrane permeability?

A

Ions

144
Q

What type of energy is used during active transport?

A

ATP or PMF

145
Q

How do nutrients move along the gradient during active transport?

A

Against their gradient from an area of Low to High concentration

146
Q

What structures are used during active transport?

A

Carrier proteins called permeases

147
Q

What does ABC stand for in ABC transport?

A

ATP binding cassette

148
Q

What domains use ABC transport?

A

All three

149
Q

What are the components of the ABC transport?

A
  1. Transmembrane channel protein
  2. Two ATP binding domains
  3. Substrate binding protein
150
Q

What does the ATP binding domain do?

A

It links the hydrolysis of ATP to the process of the molecule’s movement

151
Q

What happens during ABC transport?

A

When ATP binds to the protein, it changes shape, which triggers the conformational change of the integral protein which allows the passage of the molecule.

152
Q

What does the substrate binding protein do?

A

It captures nutrients in the periplasm or outside of the cell and transfers them to the permease channel

153
Q

How does a cell increase its chance that it will capture a nutrient in the periplasm?

A

It makes many copies of the substrate binding protein so that the chance of the nutrient bumping into this protein is high

154
Q

What is group translocation?

A

Substances (usually sugars) are chemically modified during transport into the cell

155
Q

What is the best studied example of group translocation?

A

Sugar phosphotransferase system (PTS)

156
Q

What is the energy source for PTS?

A

Phosphoenolpyruvate (PEP)

157
Q

Where is PEP found in respiration?

A

As an intermediate in glycolysis

158
Q

Why is PEP used as an energy source?

A

Because it contains a high energy phosphate bond

159
Q

What does PEP do during respiration?

A

It is used in glycolysis to make pyruvic acid

160
Q

What is efflux?

A

Pumping things out of the cell

161
Q

What is influx?

A

Pumping things into the cell

162
Q

How many proteins are involved in group translocation?

A

A group of enzymes: One transmembrane protein and several proteins inside the cell

163
Q

What is the cost to the cell during group translocation?

A

The cost is energy because the cell breaks the high energy phosphate bond of PEP to transport nutrients (glucose) instead of to make ATP

164
Q

What happens to the phosphate group during group translocation?

A

It is passed to a protein associated with the membrane. When this protein gets the phosphate, it undergoes a conformational change and allows the nutrient to be passed through the cell membrane

165
Q

What is a siderophore?

A

Organic molecules secreted by some bacteria and fungi to bind to Fe+3

166
Q

Is ferric iron soluble or insoluble?

A

Insoluble

167
Q

How does the siderophore help the organism?

A

It binds to Ferric iron to form a complex that binds to specific cell surface receptors, which then transports the iron into the cell

168
Q

Why does a cell need iron?

A

To make cytochromes and certain enzymes, like nitrogenase

169
Q

Why is iron hard to transport into a cell?

A

Insoluble (usually in solid form), large in size, charged, low abundance in the environment

170
Q

How does a siderophore encounter iron?

A

It gets released into the environment and attaches to iron and changes its solubility.

171
Q

What kind of reproductive process do eurkaryotes use?

A

Asexual and sexual

172
Q

What is asexual reproduction?

A

The cell cyle - interphase, mitosis, cytokinesis

173
Q

What is sexual reproduction?

A

Haploid gametes - meiosis

174
Q

What kind of genomes do bacteria and archaea have and what does this mean?

A

Haploid genomes, 1 version of every gene

175
Q

What is the most common asexual process that prokaryotes use?

A

Binary fission

176
Q

What are the steps of binary fission?

A
  1. Parent prepares for division by enlarging overall volume
  2. Septum begins to grow inwards as chromosomes move towards opposite ends of the cell.
  3. Septum is synthesized completely through the cell center and CM patches itself so that there are two separate cell chambers.
  4. Daughter cells divide - some species divide completely and some remain attached forming cellular arrangements
177
Q

What are the two parts to the bacterial cell cycle?

A
  1. DNA replication and partitioning

2. Cytokinesis

178
Q

Why is a bacteria’s DNA replication simpler than a prokaryotes?

A

Because they only have one chromosome rather than 26

179
Q

What are the two structures on the bacterial DNA that function in replication?

A

The single origin of replication and the terminus

180
Q

How does a DNA replicate in terms of direction?

A

Directional from the origin

181
Q

How do chromosome copies segregate in prokaryotes?

A

MreB plays a role in segregating DNA

182
Q

How does MreB function?

A

The origins of chromosomes associate with MreB tracks, and their attachment causes the fiber to elongate (their subunits are pushed farther apart).
As the fiber moves further apart, the chromosomes are separated further

183
Q

What would happen to the cell shape if MreB was mutated?

A

Since MreB gives a cell a bacillus shape, a mutated gene for MreB would produce a coccus

184
Q

How do plasmids move to opposite ends of the cell?

A
  1. Plasmid replicates
  2. ParM is anchored to ParC and ParR which attach to the origin of each plasmid
  3. ParM elongates, thereby pushing each plasmid to the poles
  4. The cell then divides with copies of the plasmid in each daughter cell
185
Q

When are Par proteins synthesized?

A

When the cell is ready for division

186
Q

What does ParM look like? ParC and ParR?

A

ParM looks like a string connecting two plasmids

ParC and ParR are the dots on the end of the string in between the string and the plasmids

187
Q

What protein is involved in prokaryotic cytokinesis?

A

FtsZ

188
Q

What is MreB homologus to?

A

Actin

189
Q

What is FtsZ homologous to?

A

Tubulin

190
Q

What does FtsZ do during cytokinesis?

A

It polymerizes to form a Z ring around the middle of the cell. When it depolymerizes, the ring gets smaller, which pinches the cell in two

191
Q

Why can studying FtsZ be beneficial to us?

A

Because it only occurs in prokaryotes therefore it is a good drug target - if the FtsZ doesn’t function properly, the cell can’t divide and the population can’t grow

192
Q

What kinds of cells use FtsZ?

A

All bacteria and some archaea

193
Q

What does growth typically refer to in microbiology?

A

Usually population growth and not growth of individual cells

194
Q

What is the batch culture?

A

A closed vessel with a single batch of medium - what we do in lab - new nutrients are not added, when they are used up, the cells die, and when wastes build up to toxic levels, the cells die

195
Q

What are the four phases of the growth curve?

A
  1. Lag phase
  2. Exponential phase
  3. Stationary phase
  4. Senescence and death phase
196
Q

What is a continuous culture?

A

An open environment where cultures are grown - a better representation of the natural environment

197
Q

What is an example of a continuous cutlure?

A

A chemostat

198
Q

What is a chemostat? How can you influence the growth curve?

A

A container where new nutrients are input and waste is syphoned out as output.
You can keep your experiment in the exponential or stationary phase by regulating the rates of input and output to the system

199
Q

What are the labels on the graph of the growth curve?

A

LOG cell number versus time

200
Q

What is the lag phase?

A

The time between inoculation and first signs of growth; cells are preparing to grow

201
Q

How does a new versus old inoculum effect the length of the lag phase?

A

An old inoculum takes longer to grow, and also if the environment is different, the cells may take longer to adjust and longer to grow

202
Q

What is the exponential phase? What is another name for it?

A

Log phase is when the cell numbers double in constant intervals; here the cells are most sensitive to antibiotics

203
Q

What is the stationary phase?

A

No net increase in cell number - # of growing cells=# of dying cells; active cells stop reproducing and metabolic activities slow down

204
Q

What is the stationary phase?

A

No net increase in cell number - # of growing cells=# of dying cells; active cells stop reproducing and metabolic activities slow down

205
Q

What is generation time? What is another name for it?

A

Doubling time is the time it takes for a bacterial cell to grow and divide or the time it takes to the population to double

206
Q

What factors can influence generation time?

A

Temperature, pH, nutrient level, type of media

207
Q

What is the equation for generation time?

A

Number of cells produced after a given number of generation = 2^n where n=number of generations

208
Q

If the generation time is one hour, how many cells are produced in 12 hours?

A

2^12

209
Q

Which domain has a longer generation time in general?

A

Eukarya

210
Q

What is exponential population growth?

A

The population doubles every generation

211
Q

Why do we graph using the log number of cells?

A

It gives us a straight line instead of a curve which helps to better display the drastic increase

212
Q

What are three ways to measure microbial growth?

A

Measuring cell number or mass by:

  1. Directly quantifying the number of cells
  2. Viable counting methods
  3. Quantity mass
213
Q

What are two ways to directly quantify cell numbers?

A

Microscopy/counting chambers

Electronic counters

214
Q

What are two ways of viable counting methods?

A

Viable plate count

Membrane filtration

215
Q

What is a way to quantify cell mass?

A

Spectrophotometry

216
Q

How can you count the number of cells using a microscope?

A

Use a specialized slide with a groove that you fill with a known volume of sample, then put the cover slip with a grid over it.

217
Q

What are the pros and cons to directly counting cells with a microscope?

A

It is inexpensive, but it takes a long time and you can’t distinguish between living and dead cells

218
Q

How does an electronic counter count the number of cells?

A

The sample is forced through a small hole, past an electrical current - the passing cell increases resistance of the current, and the counter then counts it

219
Q

How big is the channel where you pass the sample through in an electronic counter?

A

One cell thick

220
Q

What is the best counter for larger eukaryotic cells?

A

Coulter counter

221
Q

What is a flow cytometer?

A

A sensitive counter that uses a laser to count. The cells passed through are fluorescent and excite the laser, which can then detect and count the cell

222
Q

What is on either side of the channel in a flow cytometer?

A

The laser and the detector

223
Q

What is a viable plate count?

A

You serially dilute a solution and transfer it to a plate, counting how many CFUs grow

224
Q

Do you use viable plate count for low or high CFU/volume?

A

High

225
Q

What are we assuming when we use viable plate count?

A

That one single cell will produce one colony

226
Q

How many CFUs on a plate is a appropriate source to count?

A

30-300

227
Q

Why is the viable plate count method beneficial?

A

Dead cells won’t make colonies so you’re only counting live cells

228
Q

What is membrane filtration?

A

You transfer a concentrate of the solution to the plate from a filter (the small pores in the filter let out solution but trap the cells), then you count the colonies

229
Q

Do you use membrane filtration for low or high CFU/volume?

A

Low

230
Q

What is the great plate anomaly?

A

Microscopy of natural samples reveals far more bacteria than what grows on plates

231
Q

What is the reasoning for the great plate anomaly?

A

Microscopic methods count dead cells while viable methods do not; also in lab we grow cells in pure culture, but in nature, cells usually grow in mutualistic relationships

232
Q

How many microbial species have been cultivated in the lab?

A

Only about 1% of the planet’s species

233
Q

What is spectrophotometry? What instrument is used?

A

It quantifies turbidity using a spectrophotometer, which measures the amount of light passing through the sample

234
Q

What does it mean if there is a high light absorbance?

A

High turbidity

235
Q

What is the cell density proportional to?

A

Absorbance

236
Q

What are the pros and cons of spectrophotometry?

A

Quick and easy, but it also counts dead cells, and you need to create a standard curve to convert absorbance to CFU/ml

237
Q

How do you create a standard curve for spectrophotometry?

A

First you measure the cell concentration with another technique, then measure the absorbance of that sample and graph it

238
Q

What six factors effect growth and viability?

A 
Moisture
Solute concentration
pH
Temperature
O2 and ROS
Radiation
239
Q

What is an extremophile?

A

An organism that can grow under harsh conditions that would kill most other organisms

240
Q

How does a hypotonic solution effect survival?

A

(Lower osmotic concentration outside the cell) Water enters the cell, the cell may swell and burst

241
Q

How does a hypertonic solution effect survival?

A

(Higher osmotic concentration outside the cell) Water exits the cell and the membrane shrinks and shrivels

242
Q

In which solution would the cell wall protect the cell?

A

Hypotonic

243
Q

What kind of solution helps us preserve food?

A

Hypertonic

244
Q

How does a hypertonic solution help preserve food?

A

The food is made hypertonic relative to cells by adding salt and sugar - the water is drawn out of the cells so the cell shrinks and dies

245
Q

What is a halophile?

A

Optimal growth at more than .2 M of salt

246
Q

Where do halophiles grow?

A

Seawater, salty habitats, man made evaporation ponds (dry areas for forming salt - turn pink because haloarchaea make red pigment)

247
Q

What is an example of an extreme halophile?

A

Haloarchaea - requires 2M of salt

248
Q

Why don’t halophiles shrink?

A

Because they have an adaptation that prevents them from losing water:

  1. Their internal structures are less prone to denaturation - they have higher amounts of GC bonds in their DNA (stronger triple H bond)
  2. They can increase the solute concentration inside their cytoplasm to make themselves isotonic with their environment
249
Q

What kind of solutes do halophiles use to make their cytoplasm isotonic with their environment?

A

Compatible solutes - usually like K, not Na that might damage internal structures

250
Q

How many H bonds does AT have? GC?

A

AT has two H bonds

GC has three H bonds

251
Q

What is the optimum pH for neutrophiles?

A

5.5 - 7

252
Q

What is the optimum pH for acidophiles?

A

0 - 5.5

253
Q

What is the optimum pH for alkalophiles?

A

8.5 - 11.5

254
Q

When we talk about acidophiles, what pH are we referring to?

A

The pH of the environment is acidic, the pH of the cell’s cytoplasm is relatively neutral - the cell has some type of adaptation to keep its contents neutral

255
Q

What effect can extreme pH have on cells?

A

Denaturation

256
Q

What are three mechanisms the cell may use to maintain its internal pH?

A
  1. Pump OH-/H+ out of the cell
  2. Prevent the entry of OH-/H+ using a monolayer
  3. Alter the habitat pH by releasing acids or bases
257
Q

What is an example of an acidophile?

A

Helicobacter pylori

258
Q

What does H pylori cause and where is it found?

A

Found in the stomach, causes ulcers (and if you get an ulcer it increases your risk for stomach cancer)

259
Q

How does H pylori infect your stomach?

A

It is part of some people’s normal flora and is beneficial to them

260
Q

How does H pylori survive a low pH?

A

It produces the urease enzyme which converts urea to CO2 and NH3(makes environment more basic)

261
Q

How does H pylori neutralize its environment?

A

After using urease, it releases the basic NH3 to its environment which creates a cloud of neutrality around it

262
Q

Why do younger generations have less H pylori?

A

Those generations are most exposed to antibiotics - its good because H pylori can cause stomach cancer, but bad because it has proven to be beneficial in the normal flora

263
Q

Why is temperature such a huge influence on growth?

A

Bacteria can’t regulate their internal temperatures

264
Q

What happens at a microbe’s minimum temperature?

A

The membrane is gelling ,and transport processes are so slow that growth cannot occur

265
Q

What happens at a microbe’s optimum temperature?

A

Enzymatic reactions are occurring at their maximum possible rate

266
Q

What happens at a microbe’s maximum temperature?

A

Its proteins are denaturing, the cytoplasmic membrane will collapse, thermal lysis (the growth rate plummets quickly)

267
Q

What is the temperature range for a psychrophile?

A

0-20 C

268
Q

What is the temperature range for a psychrotroph?

A

0-35 C

269
Q

What is the temperature range for a mesophile?

A

20-45 C

270
Q

What is the temperature range for a thermophile?

A

55-85 C

271
Q

What is the temperature range for a hyperthermophile?

A

85-113 C

272
Q

Where are psychrophiles found? Can they grow in humans?

A

Seawater, deep ocean, fridge; can’t grow in humans, therefore they can’t cause disease

273
Q

Where are psychrotrophs found? Can they grow in humans?

A

Can grow in the fridge and in humans, therefore they are pathogens (foods)

274
Q

Where are mesophiles found? Can they grow in humans?

A

Can grow in humans, most lab organisms, can’t grow in the fridge though - pathogens

275
Q

Where are thermophiles found?

A

Hot water lines, compost piles; can’t grow in humans but might survive high heat canning process

276
Q

Where are hyperthermophiles found?

A

Hot springs, volcanoes

277
Q

What are the kinds of bacteria that can be pathogenic?

A

Psychrotrophs and mesophiles

278
Q

What is the order of the bacteria by temperature (low to high)?

A 
Psychrophile
Psychrotroph
Mesophile
Thermophile
Hyperthermophile
279
Q

What are the characteristics of Listeria monocytogenes?

A

Gram positive, nonendospore forming bacillus

280
Q

Where is Listeria monocytogenes found?

A

Soil, animal intestines, waste water

281
Q

What kind of bacteria (temperature) is Listeria monocytogenes?

A

Psychrotroph

282
Q

What disease does Listeria monocytogenes cause?

A

Listerosis

283
Q

What is listerosis?

A

Caused by the ingestion of contaminated food - examples are soft cheese, unpasteurized dairy, processed meat, raw veggies

284
Q

What happens to a healthy individual when they come in contact with Listeria monocytogenes?

A

Mild or asymptomatic

285
Q

What happens to a pregnant or immunocompromised individual when they come in contact with Listeria monocytogenes?

A

Fever, muscle aches; baby can be born with meningitis or encephalitis, stillbirth or miscarriage

286
Q

What are some examples of immunocompromised patients?

A

Very young, very old, on immunocompromising drugs, chemotherapy patients

287
Q

What kinds of adaptations do thermophiles have?

A
  1. Their protein structure is stabilized
  2. Their DNA structure is stabilized
  3. Their membrane structure is stabilized
288
Q

How is a thermophile’s protein structure more stabilized?

A

More H and disulfide bonds, chaperones (can help refold or renature proteins correctly)

289
Q

How is a thermophile’s DNA structure more stabilized?

A

Histone like proteins (wrap around DNA) and their genomes have a higher CG count

290
Q

How is a thermophile’s membrane structure more stabilized?

A

More saturated and higher molecular weight lipids, ether links, and monolayers

291
Q

What is a reactive oxygen species?

A

ROS or oxygen radical, some forms of O2 are harmful when it is easily reduced to a toxic form

292
Q

What are three examples of ROS?

A
  1. Superoxide radical (O2 ^-1)
  2. Peroxide (O2 ^-2)
  3. Hydroxyl radical (OH-)
293
Q

What are two forms of nontoxic forms of oxygen?

A
  1. Molecular oxygen (O2)

2. Covalently bound oxygen (H2O or an oxygen containing organic compound)

294
Q

What do radicals do to biological molecules?

A

ROS steal electrons from other biological molecules, oxidizing their cellular material and causing damage

295
Q

How can you tell that a molecule is an oxygen radical by looking at it written out?

A

It has an unpaired electron

296
Q

How do organisms living in oxygenated habitats survive ROS?

A

Detoxifying enzymes

297
Q

What are three examples of detoxifying enzymes and what do they produce?

A
  1. Superoxide dimutase - H2O2 and O2
  2. Catalase - H2O and O2
  3. Peroxidase - H2O
298
Q

Which enzyme requires another enzyme?

A

Superosize dimutase requires a second enzyme because it produces H2O2, which is also a ROS

299
Q

Which enzyme is easy to test for and why?

A

Catalase because it releases oxygen gas which bubbles

300
Q

What is an obligate anaerobe?

A

It requires high levels of oxygen to live

301
Q

What is a facultative anaerobe?

A

It can grow with or without oxygen, but prefers it

302
Q

What is an obligate anaerobe?

A

It does not use oxygen for growth, and oxygen is toxic to it

303
Q

What is an aerotolerant anaerobe?

A

It can grow in the presence of oxygen but does not use it for growth

304
Q

Does an obligate anaerobe produce detoxifying enzymes?

A

No

305
Q

Does an aerotolerant anaerobe produce detoxifying enzymes?

A

Yes

306
Q

What are microaerophiles?

A

Requires oxygen for growth but can only sruvive in low levels of oxygen

307
Q

Does a microaerophile produce detoxifying enzymes?

A

Yes, but only low levels

308
Q

What would happen if a microaerophile was placed in a high oxygen content environment?

A

It could only degrade so many ROS so eventually it would get overwhelmed and die

309
Q

Growing at the top of the tube only?

A

Obligate aerobe

310
Q

Growing well at the top of the tube and a little throughout?

A

Facultative anaerobe

311
Q

Growing throughout the tube?

A

Aerotolerant anaerobe

312
Q

Growing only at the bottom of the tube?

A

Obligate anaerobe

313
Q

Growing only a little ways down the tube?

A

Microaerophile

314
Q

How can you create an anaerobic environment?

A

Reducing media, work station with an incubator, gas pack anaerobe system

315
Q

What ingredient is key in reducing media?

A

Thioglycollate which reduces and removes oxygen to water

316
Q

How does an anaerobe chamber create an anaerobic environment?

A

It is flushed with inert gas - H2 reduces the O2 to water (must be careful not to let H2 go because it is explosive)

317
Q

What are two ways you can grow a microaerophile?

A

Candle Jar

CampyPak system

318
Q

How does the candle jar create a microaerophilic environment?

A

The candle burns O2, but once the O2 levels are low enough, there is not enough O2 to sustain the flame so the candle goes out. The O2 level is low now and remains the same

319
Q

How does a CampyPak system create a microaerophilic environment?

A

It uses H2 packets that reduce O2 to water, but only in low levels

320
Q

What classification do microaerophiles also fall under, and what does this mean?

A

Capnophiles - they require high levels of CO2

321
Q

Where can you find capnophiles?

A

The intestinal and respiratory tracts

322
Q

What is the order of the electromagnetic spectrum, from shortest to longest wavelength?

A
  1. Gamma
  2. Xrays
  3. UV
  4. Visible
  5. Infared
  6. Radiowaves
323
Q

What kind of rays use ionizing radiation?

A

X rays and gamma rays

324
Q

What does ionizing radiation do?

A

It can penetrate a few layers deep and cause mutations and death; it disrupts the chemical structure of many molecules, including DNA

325
Q

What kind of rays do we use on food?

A

Gamma rays - they kill most surface microbes involved in spoilage, but this is why people cook their beef all the way through

326
Q

What two kinds of bacteria can survive radiation?

A

Endospores and Deinococcus radiodurans

327
Q

How does Deinococcus radiodurnas survive radiation?

A

Its DNA repair proteins are very stable and aren’t damaged from radiation and survive to repair the cell

328
Q

What does UV radiation do to the cell?

A

It causes damage at the DNA level, causing the formation of pyrimidine dimers in DNA

329
Q

What are pyrimidine dimers?

A

Adjacent pyrimidines within he same strand of DNA become covalently linked

330
Q

What is a pyrimidine? What is a purine?

A

A pyrimidine is a one ring TC

A purine is a two ring AG

331
Q

What happens when a covalent bond forms between pyrimidines?

A

The DNA strand kinks, which affects the structure and function of the DNA

332
Q

What are biofilms?

A

Microbes growing on a surface

333
Q

What are biofilms coated with?

A

Extracellular polymeric substances (EPS, slime)

334
Q

What is the most common way bacteria grow in nature?

A

Biofilms

335
Q

How can you remove a biofilm?

A

It is very difficult and it requires physical abrasion

336
Q

When do cells produce EPS?

A

After they attach to the surface

337
Q

How are biofilms beneficial to bacteria?

A
  1. Hard to remove
  2. Can use neighbors waste as nutrients and energy source
  3. Can use EPS as energy source
  4. Provides protection from viruses, predators, and antibodies
338
Q

Why are biofilms studied?

A

Pathogenesis - biofilms can grow in a catheter

Environmental quality - biofouling

339
Q

What is biofouling?

A

When an organism degrades or oxidizes property, such as docks, boats, pipes, or anything that gets wet

340
Q

What is quorum sensing?

A

The mechanism by which bacteria assess their population density

341
Q

What does quorum sensing ensure?

A

That there are a sufficient number of cells present before the population initiates a response requiring a certain cell density

342
Q

How is quorum sensing specific?

A

Cells release a chemical signal that allow them to talk to each other that is specific to their species

343
Q

What are three examples of quorum sensing?

A

Toxin production, bioluminescence, biofilm formation

344
Q

What is the term for the chemical signal?

A

Autoinducer

345
Q

What is an example of an autoinducer?

A

Acylhomoserine lactones (AHL) - there are many different types

346
Q

What happens when there is a high cell and high autoinducer density?

A

The quorum sensing genes are expressed and the cells exhibit the group behavior

347
Q

When does an autoinducer reach high concentrations inside the cell?

A

Only when many cells are near

348
Q

How could antiquorum sensing drugs be beneficial?

A

They could block the transmission and receiving signal, and therefore the bacteria couldn’t turn on its group behavior of toxicity - it would only harm the bacteria, and not your own cells

From Flashcardlet (133 decks)

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