L1: Phylogeny and Morphology of Bacteria Flashcards Preview

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Flashcards in L1: Phylogeny and Morphology of Bacteria Deck (153):
1

What is the traditional definition of a prokaryotes in terms of:
Chromosome number:
Chromsome ploidy:
Chromosome shape:
Nuclear membrane presence:
Mitosis occurrence:
Ribosome size:
Mitochondria, ER presence:
Phagocytosis occurring:
Sterols in membrane:

Chromosome number: 1
Chromsome ploidy: Haploid
Chromosome shape: Circular
Nuclear membrane presence: No
Mitosis occurrence: No
Ribosome size: 70S
Mitochondria, ER presence: No
Phagocytosis occurring: No
Sterols in membrane: No

2

What is the traditional definition of eukaryotes in terms of:
Chromosome number:
Chromsome ploidy:
Chromosome shape:
Nuclear membrane presence:
Mitosis occurrence:
Ribosome size:
Mitochondria, ER presence:
Phagocytosis occurring:
Sterols in membrane:

Chromosome number: >1
Chromsome ploidy: Dipoid or higher
Chromosome shape: Linear
Nuclear membrane presence: Yes
Mitosis occurrence: Yes
Ribosome size: 80S
Mitochondria, ER presence: Yes
Phagocytosis occurring: Yes
Sterols in membrane: Yes

3

What problems have arisen with the traditional definition of prokaryotes? (4)

1. Many bacteria have >1 chromosome
2. Ploidy is variable based on growth rate
3. Many bacteria have linear chromosomes
4. Shouldn't use negatives to define a category

4

What is the only remaining defining feature of bacteria?

Ribosome size

5

What is the ribosome made of?
What does this mean for defining bacteria?
What does this mean for evolution?

RNA
Differences between pro and euk are differences in RNA composition.
Can use nucleotide sequencing to determine the evolutionary relationships of all organisms

6

Using recent analysis, what has the traditional all-encompassing kingdom of prokaryotes been split into?

(Eu)Bacteria
Archaea

7

All known human bacterial pathogens are from what domain of prokaryotes?

Eubacteria

8

All of the kingdoms of eukaryotes have been united into what?

Eukarya domain

9

Which has more subdivisions, eukarya or the two prokaryotic domains?
What does this mean?

Two prokaryotic domains

Bacteria are more diverse than eukaryotes

10

The genomes of chloroplast and mitochondria are related to many bacterial species, suggesting what?

That the endosymbiotic theory of eukaryotic cellular evolution is correct.

11

Do the vast majority of bacteria have any impact on humans?

No

12

Bacteria are critical for what two things? (2)

1. Recycling of environmental materials
2. Maintaining a healthy environment

13

Can bacteria be domesticated?

Yes such as in fermentation of alcohol

14

Of the few bacteria that interact with humans, are most harmful, harmless, and/or beneficial?

Harmless or beneficial

15

These bacteria that are harmless or beneficial to humans are called what?

Natural flora

16

In the human body, how do the cell numbers of human cells and bacterial cells compare?

10X more bacterial cells than human cells in human body.

17

In the human body, how do gene numbers of human genes and bacterial genes compare?

100X more bacterial genes than human genes in body.

18

What is the rigidity of the bacterial cell wall due to?

Peptidoglycan

19

Which is the first big stain to use when determining bacteria?

Gram stain

20

The gram stain separates cells based on what?

Being either Gram positive or Gram negative which is based on their cell wall architecture

21

Relatively speaking, how many bacteria have peptidoglycan in their walls?

Nearly all

22

What does a peptidoglycan consist of?

1. Peptide: Amino acids
2. Glycan: sugars

23

The glycan portion of peptidoglycan consists of what? (2)

1. N-acetylglucosamine (NAG)
2. N-acetyl-muramic acid (NAM)

24

What are the two exceptions to bacteria with peptidoglycan in their cell walls?

1. Mycoplasma
2. L-Forms

25

Describe the organization of the sugars in peptidoglycan?

Alternating NAG and NAM

26

Describe the organization of peptide in peptidoglycan.

A chain of mixed D- and L- amino acids attached to NAM with a di-amino acid in the third to last position and ending with D-ala-D-ala.

27

what is a di-amino acid? (2)

1. lysine
2. diaminopimilic acid

28

Is the composition of the D- and L- amino acids always the same for bacterial peptidoglycan?

No, varies by species

29

How does cross linking occur between peptides of the same peptidoglycan?

The penultimate D-ala of one peptide chain joins with diamino acid of another which causes deletion of the terminal D-ala of the first.

30

Does the peptide bridge vary much?

Yes, from direct linkage between the two peptides to several amino acids

31

What allows for the crosslinking between glycan chains?

The peptide chain flexibility

32

Purpose of crosslinking of peptidoglycans?

Formation of meshwork that provides tensile strength necessary to (1) restrain the cytoplasm and (2) give the cell shape.

33

What pressure does crosslinking try to combat?

Turgor pressure

34

Gram positive cell walls have what 3 main features?

1. Thick (up to 30 layers) of peptidoglycan externally
2. Wall- and lipo-techoic acids
3. Integral membrane proteins

35

Is PTG permeable?

Yes

36

Which have a higher internal osmotic pressure, gram positive or gram negative bacteria?

Gram positive

37

In layman's terms, what are wall- and lipo-techoic acids?

Repeating sugar phosphate chains

38

Function of wall-and lipo-techoic acids?

Give cell negative charge in order to attract positive charges adding strength to the wall

39

Do gram-negative cells have wall- and lipo-techoic acid?

No

40

3 components of gram-negative cell wall?

1. Outer membrane
2. Thin peptidoglycan layer
3. Peri-plasm separating inner and outer membranes and contains the peptidoglycan and proteins for processing solutes

41

What does the outer membrane act as for gram-negative bacteria?

Permeability barrier

42

The outer membrane of gram-negative bacteria consists of what four parts?

1. Phospholipids like those in inner membrane
2. Lipoproteins: Attach PTG layer to Outer
3. Porins: Allow some diffusion
4. Lipopolysaccharide

43

What are the 4 parts of lipopolysaccharide?

1. O-antigen
2. Core polysaccharide
3. Disaccharide diphosphate
4. Fatty acids

44

Together, the disaccharide diphosphate and fatty acids of LPS make up what?

Lipid A

45

Lipid A of LPS is known as what?

Endotoxin

46

Result of Endotoxin in the blood?

Fever, shock, and death during gram-negative infections

47

The O-Antigen has what significance in immunology?

It is a major antigenic determinant and is used to characterize bacteria

48

What are the five steps of a gram stain.

1. Fixation
2. Crystal violet
3. Iodine treatment
4. Decolorization
5. Counter stain of safranin

49

What is the key step of a gram stain?

Decolorization step

50

How does decolorization affect both gram positive and gram negative?

Gram positive: Dehydrates the PTG thus trapping the stain
Gram negative: Strips the outer membrane from the cell allowing the primary stain to escape

51

Mycoplasma stain what?

Gram negative even though they are closer to Gram-positive since they dispensed with a cell wall

52

What color is gram positive?

Purple

53

what color is gram negative?

Pink

54

Describe the set up of a mycobacterial cell wall

Gram positive cell wall with an outer membrane that is NOT similar to a gram negative OM.

55

Mycobacterial cell wall consists of what 3 things?

1. Thick peptidoglycan layer
2. Arabinogalactan (sugar) layer
3. Mycolic acids/Wax D

56

What 3 main bacteria don't have a cell wall

1. Mycoplasma
2. L-forms
3. Domain archaea

57

What causes mycoplasma to have such a strong membrane?

Sterols

58

What do archaea have instead of peptidoglycan?

Pseudopeptidoglycan

59

Why don't mycobacteria stain well?

Stains can't penetrate the mycolic acid wax

60

How does one stain for mycobacteria?

Acid fast stain

61

What are the steps of the acid fast stain?

1. Carbol Fuchsin primary stain steamed in to penetrate the membrane and stian the cells red.
2. Acid alcohol leaches the stain out of all cells that are NOT mycobacteria
4. Methylene blue counterstains the leached cells

62

What shape is coccus?

Spherical

63

What bacteria are in cocci? (5)

1. Strep
2. Staph
3. Pneumococcus
4. Gonococcus
5. Meningococcus

64

What shape is bacilli or rod?

Cylindrical

65

What bacteria are bacilli/rods? 2

anthrax
bacillary dysentery

66

What shape is coccobacilli?
What bacteria is this?

Small rods
E. coli

67

What shape is vibrios?
What bacteria is this?

Comma-shaped
Vibrio cholerae

68

What shape is spirillae?

Spiral-shaped

69

Which bacteria are spirillae?

Treponemes
Borrelia

70

What are the four most common organizations of pathogenic bacteria?
And example of each

1. Tetrads of cocci: Micrococcus
2. Diplococcus (two cocci): Strep pneumoniae
3. Streptococcus (cocci in chains): Group A strep
4. Staphylococcus (cocci in clusters): S. aureus

71

Bacterial colonies are most often developed on what?

Agar plate

72

What is a bacterial colony?

Mass of cells that arise from a single cell

73

What makes up a flagellum?

Protein

74

Flagella are responsible for what?

Motility

75

What direction do flagella move?

Rotary/Propellar-like

76

Flagellum is actually a polymer of a single protein called?

Flagellin

77

Can flagellum help bacterial pathogenesis?

Yes!

78

What is it called if the bacteria only has one flagellum?

Monotrichous

79

What is it called if the bacteria has many flagellum?

Peritrichous

80

which is longer, pili or flagellum?

Pili

81

Which is thicker, pili or flagellum

Flagella

82

How are pili composed?

Protein subunits of pilin protein

83

3 functions of pili?

1. Attachment to host or other bacterial cells
2. Movement (twitching motility)
3. Conjugation DNA transfer

84

What is the other word for pili?

Fimbria

85

What are the two types of pili and what is each involved in?

1. Common pili = attachment
2. sex pili = hollow for conjugation transfer

86

Define a capsule

Polysaccharide or poly-glutamic acid layer outside of the OM in Gram- bacteria and outside PTG in Gram+ bacteria

87

What is the general function of a capsule?

Protection from host defenses

88

What is a slime layer or glycocalyx?

Outer polysaccharide layer that adheres lsess firmly to cells

89

DIfference between glycocalyx and capsule?

Capsule: Distinct gelatinous layer
Slime: Irregular diffuse layer

90

Does the chemical structure of glycalyx and capsules differ across different bacteria?

Yes: allows for antigenic characteristics used in determining bacterial strains

91

Define endospore

Non-replicating resting cell that is highly resistant to environmental stresses

92

What can an endospore withstand? (4)

1. Boiling
2. Radiation
3. Chemicals
4. Drying

93

Endospores are the result of what?

Program that replaces a vegetative cell with a spore?

94

Are endospores reproductive spores?

No

95

How many spores can a mother cell create?

Just one

96

What will cause a cell to come out of being an endospore?
What is this process called?

If conditions improve (less stress)

Germination

97

What is the primary reason for sterilization and autoclaving?

Killing spores

98

Can spores last a long time?

Decades, centuries

99

Why was canning introduced?

Elimination of spores

100

All bacteria require what six elements for growth?

CHNOPS

101

Which element is most useful in distinguishing bacteria?

Carbon

102

Bacteria capable of direct use of CO2 are called?

Autotrophs

103

Bacteria that must obtain carbon from organic carbon are called?

Heterotrophs

104

Bacteria that use light as a source of energy are called?

Phototrophs

105

Bacteria that use chemicals as a source of energy are called?

Chemoautotroph

106

Bacteria that use inorganic chemicals are called?

Lithotrophs

107

Bacteria that use organic chemicals are called?

Organotrophs

108

All known disease-causing bacteria are what category?

Chemo- and organo-heterotrophs

109

Two ways bacteria are separated by oxygen?

1. Whether O2 is used in metabolism (respiration, fermentation)
2. Whether the bacterium can detoxify oxygen

110

End products of fermentation include? (6)

1. lactic acid
2. ethanol
3. butyric acid
4. propionic acid
5. 2,3-Butanediol
6. Mixed acids

111

Fermentation products are produced in a series of reactions whose goal is what?

Production of terminal electron acceptors

112

What is bacterial respiration?

Same as normal biochem except that some bacteria can use other chemicals other than nitrate as the final electron acceptor.

113

How does fermentation differ from respiration? (3)

1. Organic compound as final electron acceptor
2. Can only do substrate level phosphorylation which is inefficient
3. Pyruvate is central intermediate but end products can vary

114

Reduction of oxygen during during respiration leads to formation of what? (2)

1. Superoxide anion
2. Hydrogen peroxide

115

What detoxifies the toxic superoxide anion and hydrogen peroxide in bacteria? (2)

1. Superoxide: Superoside dismutase
2. H2O2: Catalase

116

What will the catalase test distinguish?

Catalase positive: Gram positive cocci Staph
Catalase negative: strep

117

What do obligate aerobes require?
Do they do fermentation?
Do they have catalase or SD?
Examples? (2)

Oxygen
No
Yes
Pseudomonas
Bacillus

118

What do microaerophilic bacteria require?
What is toxic to them?
Examples (2)

Low oxygen
Too much oxygen
Campylobacter
Helicobacter

119

What do facultative anaerobes do for metabolism?
Examples 2

Respire aerobically until oxygen is gone then ferment
Enterobacteriaceae and Staph

120

What do facultative aerobes do for metabolism?
Do they have catalase or SD?
Examples? (2)

Ferment
Lack both
Streptococci and enterococci

121

How do aerotolerant anaerobes interact with oxygen?
Example?
Do they have catalase or SD?

They are anaerobic but can tolerate oxygen for brief periods.
Actinomyces
Often SD

122

How do obligate anaerobes do metabolism?
Do they have catalase or SD?
Examples? (2)
What is a defining feature?

Ferment
Lack both
Bacteroides and Clostridia
Stink

123

What does a capnophile require?
How does one facilitate that in a lab? 2

Increased CO2

Candle jar or CO2 incubator

124

A microaerophile requires what compared to a capnophile?
How does one facilitate that in lab?

Higher CO2

Gastight jar: Chemical packet generates hydrogen and CO2

125

What other things can bacteria be categorized on? 3

1. optimum growth temperature
2. pH
3. osmotic pressure

126

4 phases of bacterial growth?

1. lag phase
2. logarithmic phase
3. stationary phase
4. death phase

127

What is the lag phase?

Period of adjustment of new medium requiring enzyme synthesis and gearing up for growth

128

Logarithmic phase involves what?

Exponentially increasing cell numbers leading to rapid accumulation of cells

129

What is the generation time?

Time it takes for one cell division cycle

130

What is the range of generation times?

20 minutes to several hours

131

Is each generation time the same for a species?

Yes

132

What is the inverse of generation time?

Growth rate

133

Why does the stationary phase occur?

Nutrients become limiting and toxic byproducts build up

134

What happens during stationary phase?

Cells change genetic program to become dormant and may make endospores.

135

Why is stationary phase important clinically?

Many bacteria become more resistant to anti-biotics

136

What is the death phase?

Death of cells due to toxic byproducts

137

What makes the body tough for exponential growth of bacteria? (2)

1. Very few areas where nutrients are plentiful
2. Very few areas where toxic byproducts will be washed away

138

Where is one place where nutrients are good and byproduct washing occurs?

Colon

139

Do in vitro and in vivo concentration differ for antibiotics?

Yes

140

What is the form that cells grow in a test tube?

Planktonic

141

What is the form that cells grow in the body?

Surface biofilms

142

What makes bilfilms so different from a culture tube?

They are complex structures of regions with metabolitcally differently acting cells

143

What are the steps of biofilm formation?

1. Planktonic cells proliferate
2. Monolayer forms
3. Type IV pili and twitching motility allows for formation of microcolony
4. Biofilm forms

144

Two things that can happen to mature biofilm?

1. Physical detachment shears a piece off
2. Mobilize to form planktonic cells again

145

Where can biofilms be found in terms of inanimate objects? (3)

1. indwelling catheters
2. artificial joints
3. anything foreignly inserted into body

146

What is resistance?

Stable genetic change that is passed down to cell progeny

147

What is persistence?

Metabolic state that allows transient tolerance to antibiotics and other stress but is not passed down to cell progeny

148

What things do you have to think about in terms of disinfectant and sterilization?

1. How it works
2. does it sterilize
3. what does it work best again
4. what does it work poorly against

149

Where is S. pyrogenes found?

URT

150

Where is S. agalactiae found?

OB/neonate

151

Where is S. pneumoniae found? 2

Upper respiratory (ear)
Lower respiratory

152

Where is E. facalis and E. faecium found?

Skin and bone

153

Where is S. mutans found?

Upper respiratory tract