Microbiology unit 2

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1

What is the function of the cyanobacterial antenna complex?

To absorb photons and transfer energy to the reaction center.

2

Sulfur oxidation causes environmental__________.

acidification due to production of sulfuric acid.

3

Cyanobacteria are the only prokaryotic phototrophs that___________.

evolve oxygen as a result of photolysis, can use H2O as an electron donor, and have both PSII and PSI.

4

For what purpose do anoxygenic phototrophs with photosystem II (PSII) reaction centers run reverse electron transport?

NADPH synthesis

5

Hydrogenotrophs use H2 in what way?

as a source of energy and electrons

6

Methanogenesis, NOT methylotrophy, is the __________.

oxidation of H2

7

Define Methylotrophy.

the oxidation of single carbon compounds by oxygen, nitrite, or sulfate.

8

Define Methanotrophy.

A special form of methylotrophy where methane is the substrate.

9

Nitrifiers obtain energy from which of the following?

the aerobic oxidation of ammonia and nitrite

10

Anoxygenic phototrophic bacteria belonging to the genus Chlorobium would likely exist in close proximity to microbes that require sulfate for which of the following?

anaerobic respiration

11

ATP production in halophilic archaea that contain bacteriorhodopsin differs from ATP production in cyanobacteria in that ONLY cyanobacteria____________.

oxidize water.

12

Photosystem proteins (regardless of the organism in which they are found) share a common ancestry with components of what other biological system?

respiratory electron transport

13

An organism contains photosystem II but not photosystem I. From this, it can be concluded that the organism__________.

can produce ATP from light energy, but not NADPH.

14

Photoheterotrophic organisms can_______________.

use light as an energy source, but must still acquire reduced carbon from the environment.

15

Methylotrophy would refer to microbial oxidation of which of the following for growth?

CH3NH2 , CH3OH, CH4

16

Define Hydrogenotrophy.

the use of hydrogen gas as an electron donor.

17

The ability to obtain energy via the oxidation of reduced sulfur compounds (e.g., H2S) is widespread among prokaryotes (both Bacteria and Archaea). Unfortunately, the nature of the major reaction end product has what effect on the immediate environment?

drastically lowers the pH

18

Is it possible to produce a proton motive force without an electron transport system?

Yes, by using a membrane-bound protein pigment capable of behaving as a proton pump.

19

Metabolism using an electron transport system is classified based on the nature of the initial electron donors and terminal electron acceptors. Lithotrophy uses __________ molecules as the __________ electron __________.

inorganic; initial; donors

20

What is the terminal electron acceptor in oxygenic photosynthesis?

NADP+

21

For every 2 molecules of water consumed, the light reactions of oxygenic photosynthesis generate_______molecule(s) of ATP,_______ molecule(s) of NADPH, and _______ molecule(s) of O2.

3,2,1

22

In photoautotrophs, the chemical energy produced by the "light" reactions (i.e., photolysis and electron transport) is used to fuel which cellular process?

carbon fixation

23

In photoautotrophs, the chemical energy produced by the "light" reactions (i.e., photolysis and electron transport) is used to fuel which cellular process?

carbon fixation

24

Which of the following groups is responsible for the vast majority of primary production on the planet?

photoautotrophs

25

List substrates of lithotrophy.

Hydrogen,

Elemental sulfur,

Methane,

Carbon monoxide,

Ferrous iron,

Ammonia

26

List substrates of Organotrophy

Gluconate,

Fatty acids,

Glycerol,

Fructose

27

Suppose you have isolated a compound that alters the quorum signal of Pseudomonas aeruginosa, such that it cannot interact with its normal receptor. Bacterial cells targeted by such a disrupter would most likely___________.

be similar to free-living cells in their sensitivity to antibiotics.

28

Pseudomonas aeruginosa represents a well-studied model organism for single-species biofilm formation. This research is also of direct medical significance because of the propensity of these bacteria to form biofilms in the______of patients with cystic fibrosis.

lungs

29

What early events in biofilm formation by Pseudomonas aeruginosa involves the extension and retraction of a specific pilus?

twitching motility

30

Many biofilm-specific phenotypes are controlled by “quorum sensing.” This system allows bacteria to regulate gene expression according to the concentration of_______in its immediate environment.

other bacteria

31

Biofilms form_____________.

to establish a collaborative community that promotes the members’ growth and reproduction.

32

Why are elements such as cobalt, copper, manganese, molybdenum, nickel, and zinc referred to as micronutrients?

All cells require these elements in trace amounts, but they don't need to be deliberately added because these elements are ubiquitous and sufficient amounts are naturally present in standard media preparations.

33

Many bacteria cannot easily be cultured from their natural habitat. Usually that is because those cells normally obtain a necessary metabolite from a host organism (or other member of the microbial community) and can no longer synthesize that requirement for themselves. Examples of such growth factors include all of the following except___________.

adenosine triphosphate

34

Because of its requirement for active transport (ABC transporters) and basic energy transformations, a cell must have some way to generate its own__________.

adenosine triphosphate

35

An essential nutrient is one that__________.

bacteria need for proper growth but cannot make themselves.

36

All organisms require_______as a macronutrient.

carbon

37

You have isolated a mutant strain of Bacillus subtilis (which you designate wimP) whose endospores can be killed by boiling water. When you analyze the endospores produced by this strain, you find that compared to endospores produced by the parent (a wild-type strain), the wimP spores have significantly__________.

higher water content.

38

Suppose the researcher who ran this experiment also measured growth of the culture by taking optical density readings using a spectrophotometer. During which phase would the data be least proportional to that in the above graph (obtained using numbers of viable cells)?

death phase

39

Cellular synthesis of___________would be directly affected by nitrogen limitation?

Nucleotides and Amino acids

40

Organisms that need to ingest reduced carbon are called__________.

heterotrophs.

41

Paenibacillus wynnii uses the oxygen produced by cyanobacteria for which cellular process?

Respiration

42

What important role(s) do cyanobacteria play?

Nitrogen-fixers and Primary producers

43

Biofilms preferentially form in __________ environments with __________ levels of nutrients.

moist / high

44

John Tyndall discovered that intermittent boiling (cycles of heating and cooling) can kill bacterial endospores. This is a result of____________.

endospores germinating into vegetative cells during the cooling phase.

45

Which of the following elements is considered a "macronutrient" even though it is not part of the basic chemical makeup of carbohydrates, lipids, proteins, or nucleic acids?

magnesium

46

While adding nutrients to a culture medium in a glass container, which of the following would LEAST likely need to be added and why?

Zinc, because it is a micronutrient

47

A complex medium is one that___________.

is nutrient-rich, but the amounts and identity of specific nutrients are unknown.

48

________are resistant to many stresses that would kill vegetative cells.

Endospores

49

The first photoautotrophs to evolve did not produce oxygen. What does this most strongly suggest about them?

They used something other than water as a source of electrons.

50

What capability is shared by many species of Gram-positive pathogens.

sporulation

51

What is the role of dipicolinic acid in endospore formation?

It aids in dehydration of the endospore and enhances heat resistance.

52

Quorum sensing does what?

Coordinates biofilm formation via chemical signaling among cells.

53

what equation is used to deal with generations of bacteria and calculating populations of cells?

N 0 × 2 n = Nt, where N 0 is the starting number of cells, n is the number of generations, and Nt is the final number of cells.

54

Biofilms are defined as microbial communities growing within a self-produced extracellular matrix composed primarily of___________.

polysaccharides

55

The number of generations per hour (k)__________

is the reciprocal of generation time (g).

56

Consider a typical growth curve of a bacterial batch culture grown in the laboratory. Which of the following phases would be shortened, or absent entirely, if the culture was started using an inoculum from a log-phase culture (in the same medium)?

lag phase

57

Bacteria as a group are incredibly metabolically diverse, but individual species are often highly specialized to reduce competition in their natural environment. This results in these species being unculturable because____________.

their growth may depend on necessary growth factors provided by other organisms in their natural environment

58

What is the correct order of phases of growth is after a growth of bacteria inoculated into a new culture medium?

lag, log, stationary, death.

59

For many bacterial types, this component is an absolute requirement for growth, for others it may be toxic, and still for others, some can live with or without it. This component is_______.

O2

60

The engulfment by the mother cell and deposition of dipicolinic acid highlight this process.

endospore formation

61

nutrient addition at mid to late log phase allows for further increase in cell yield:

fed-batch culture

62

Cellular communication & exopolysaccharide production characterize this.

biofilm formation

63

When severely stressed, these bacteria produce highly resistant dormant forms.

Bacillus and Clostridium

64

If an inoculum of a particular bacterial species were transferred to a shake flask containing a liquid growth medium lacking an essential nutrient, which growth pattern would likely be observed?

no growth would occur at all

65

Bacteria capable of thriving in aquatic environments where the external osmolarity is very high would likely be considered________.

halophilic

66

_________agents are the same in that both would always yield a decrease in viable count when applied to a susceptible bacterial culture.

Bacteriocidal and bacteriolytic

67

Bacteria have higher D-values for irradiation than protists because bacteria have_________.

smaller genomes

68

What is the primary method used by microbes to have water cross the membrane?

aquaporins

69

Halophiles must have_______NaCl levels to grow.

10%-20%

70

________kills all cells, spores, and viruses on an object.

Sterilization

71

_________removes pathogens from inanimate surfaces.

disinfection

72

___________removes pathogens from the surface of living tissues.

Antisepsis

73

Oxygen exposure will kill________

Strict anaerobes

74

Microbes can develop resistance to chemical control agents if_____________.

low concentrations of the chemical are applied to reduce the number of microbes below target number.

75

Chemical disinfectants are intended for_____________.

non-living surfaces, and can damage macromolecules in a microbial cell.

76

Barophilic prokaryotes are found primarily_____________.

deep in the ocean.

77

An organism that grows best at high osmolarity is called____________.

a halophile.

78

An organism that grows best in cold environments is called____________.

a psychrophile

79

In__________water will flow out of the bacteria by osmosis. This will decrease cell volume.

a hypertonic solution

80

In__________water will flow into a bacterium by osmosis.

a hypotonic solution

81

In an_________ the bacterium is at water equilibrium with its environment.

an isotonic solution

82

What explains why the death of microbes follows a negative exponential curve?

The cells accumulate random lethal hits to essential proteins or genes at a specific rate.

83

A steam autoclave attempts to kill bacteria through a combination of____________.

high temperature and high pressure.

84

Aerobes may tolerate the presence of oxygen because they have the enzyme____________.

superoxide dismutase

85

Pasteurization limits microbial numbers through_____________.

high heat.

86

Which of the following adaptations is most important in helping microbes be successful in an extreme environment such as a very low pH that would harm normal microbes?

Altered proteins to allow them to function better in that environment

87

An organism growing in hot sulfur springs is often also_______.

An acidophile.

88

What protein characteristic would be best for psychrophilic microbes?

flexibility

89

Which of the following is used as the standard for pasteurization, and why is it used as the standard?

The ability to kill Coxiella burnetii since it is the most heat-resistant pathogen that doesn't form spores.

90

Hydrogen peroxide used as a 6% solution is used to clean wounds on skin as a(n) __________, and it is also used as a stronger solution (>30%) as a(n) __________.

antiseptic; disinfectant

91

Proteins have optima for___________.

temperature, pH, and osmolarity

92

What are the function(s) of the viral capsid.

It determines the shape of the virion, and protects the viral genome.

93

The viral capsid is comprised of_____________.

proteins

94

Viroids lack________

proteins

95

What are viroids?

Naked nucleic acids, usually RNA, devoid of a protein capsid. Some plant viroids are ribozymes, capable of catalytic action.

96

What are capsids?

protein shells that surround the viral genome.

97

Which viral genome is likely to require an RNA-dependent RNA polymerase for transciption upon viral entry?

(–) sense single-stranded RNA

98

Reverse transcriptase catalyzes _____ production from a _____ template.

DNA; RNA

99

Control sequences in DNA do not code for proteins, but rather they___________.

Serve to regulate gene function

100

The replication of the circular prokaryotic chromosome utilizes two replisomes each of which contains___________.

2 DNA polymerase molecules, a DNA primase, & a DNA helicase.

101

The replication of the circular prokaryotic chromosome results in_________which must be resolved to form two separate chromosomes.

catenane formation

102

The lagging strand is synthesized______, and the leading strand is synthesized______.

5’ to 3’, 5’ to 3’

103

The replication of the circular prokaryotic chromosome requires the activity of__________.

RNase H, replacement with DNA, and DNA ligase activity.

104

_____________form the sugar phosphate backbone of DNA.

Phosphodiester bonds

105

T/F: The 5’ phosphate at the end of one strand will be directly opposite to the 3’ hydroxyl (‐OH) end of the complimentary
strand.

True

106

T/F: One strand of DNA contains purine bases that hydrogen bond to the complimentary strand containing pyrimidine bases.

False

107

_____exists as a single strand that may complimentary base pair with itself to form different structures.

RNA

108

T/F: The stability of DNA is much greater than that of RNA.

True

109

Plasmids of high copy number are_____likely to be passed on to daughter cells following cell division.

less

110

_______typically carry hundreds of genes, usually of multiple metabolic pathways.

Plasmids

111

The presence of_______is usually not a factor that affects the ability of a cell to maintain a plasmid.

selective pressure

112

List things required for prokaryotic transcription?

sigma factor,

core RNA polymerase,

promoter

113

What can cause transcription to end?

...

114

What is the importance of the stop codon UAG?

It tells the ribosome to stop translating the mRNA.

115

The __________ of transcription and translation helps microbes rapidly adjust gene expression to changes in their
environment.

coupling

116

After __________, each polypeptide must be properly folded and placed at the correct cellular or extracellular location.

translation

117

T/F: The DNA that comprises prokaryotic genomes has been acquired solely from prior generations.

False

118

The presence of competence factors, the formation of translocasomes in the cell membrane, and the presence of extracellular DNA all indicate_________.

the cell is ready to carry out transformation.

119

An______is capable of transferring a portion of the chromosome during conjugation.

Hfr strain

120

Regarding conjugation an Hfr strain has an______integrated in its chromosome.

F factor

121

Conjugation requires physical contact between cells via the formation of a______.

sex pilus

122

Bacterium X has acquired an F prime factor from bacterium Y via conjugation. This means that_________.

bacterium X has acquired a gene or genes from the chromosome of bacterium Y

123

T/F: In the mechanism of general transduction, only few specific genes from a bacterial chromosome may be passed one from one cell to another via a bacteriophage.

False

124

E________can occur between a cell’s chromosome and DNA acquired via conjugation, transduction, or transformation.

Recombination

125

Recombination requires_______to scan for homology between the chromosome and acquired DNA.

RecA protein

126

Recombination results in the formation of_________.

Holiday structures.

127

What typically results in an increase in the size of the chromosome?

recombination

128

What can integrate into different regions of the same chromosome or into a different chromosome?

transposable elements

129

What has a gene that codes for a transposase enzyme that facilitates transfer of the segment.

transposable elements

130

________may be replicated and the copy integrated elsewhere, or it may excise altogether and “jump” to a new location.

transposable elements

131

________are flanked by inverted repeat sequences.

transposable elements

132

Define transposable elements

DNA segments that are mobile. They can replicate and insert copies at sites within the same or a different chromosome. They can therefore alter the genetic constitution of an organism.

133

What is the process that turns off the transcription of a gene or genes?

Repression

134

What uses the Z pathway?

Cyanobacteria and chloroplasts

135

Define photolysis

The decomposition or separation of molecules by the action of light.

136

What are Halobacterium?

Archaea that live in high salt environments.

137

What are Bacteriorhodopsin?

Protein used by Archaea, most notably by Halobacteria, that acts as a proton pump which captures light energy and uses it to move protons across the membrane out of the cell.

138

Sensory rhodopsin direct the cell toward_____and away from______.

orange light;blue or ultraviolet light

139

Nitrifiers do what?

Oxidize ammonia, generationg nitrates, nitrites, which are converted to acids.

140

Sulfolobus are archaea that oxidize______to______.

H2S; Sulfuric acid

141

Hydrogenotrophy is when__________.

Hydrogen is used as the ETS e- donor. Used by heterotrophs and lithotrophs.

142

Chlorophylls of plants_____green light while bacteriochlorophylls_____green light with carotenoid pigments.

reflect;absorb

143

Light capture maximized by arranging chlorophyll molecules into__________.

antenna complexes

144

A_________is a membrane-bound compartment inside chloroplasts and cyanobacteria. They are the site of the light-dependent reactions of photosynthesis.

thylakoid

145

List required macronutrients.

C,H,O,N,P,S

146

List required micronutrients.

Co, Cu, Mn, Mo, Ni, Z

147

________is growth of a pure culture.

Axenic growth

148

What are prototrophic bacteria?

Wild type strain, not requiring specific nutritional substances for normal metabolism and reproduction

149

What are Auxotrophic bacteria?

a mutant that requires a particular additional nutrient that the wild type does not.

150

What is cellular communication based on cell density and nutrients.

Quorum sensing

151

_______is the destruction of all cells, viruses, and spores.

Sterilization

152

_______is the reduction of pathogen numbers for inanimate objects.

Disinfection

153

_________is the reduction of pathogen numbers for living tissues.

Antisepsis

154

______is basic hygenic practices.

Sanitation

155

Define bacteriostatic

Growth inhibitory

156

Define bacteriocidal

killing of cells, cells remain intact.

157

Define bacteriolytic.

Killing of cells, cells are lysed, destroyed.