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1

Macro composition in percent dry weights of protein, lipids, RNA, DNA, and saccharides

Protein: 55%
Lipids: 9%
RNA: 20%
DNA: 3%
Saccharides: 3-5%

2

Which elements are needed to synthesize oxygen molecules?

Carbon
Hydrogen
Oxygen

3

What are the 2 categories for carbon source organisms?

Autotrophs
Heterotrophs

4

Autotrophs

Get their carbon from CO2

5

Heterotrophs

Get their carbon from a source other than CO2

6

What are the 2 categories for energy source organisms?

Phototrophs
Chemotrophs

7

Phototrophs

Energy from light

8

Chemotroph

Energy from oxidation of reduced compounds (organic or inorganic)

9

What are the 2 categories for electron source organisms?

Lithotrophs
Organotrophs

10

Lithotrophs

Get electrons from reduced inorganic compounds (eg. plants)

11

Organotrophs

Get electrons from reduced organic compounds

12

What is nitrogen needed for?

Amino acids
Purines
Pyramiding
Cards
Lipids

13

What is phosphorous needed for?

Nucleic acids
Phospholipids
Nucleotides

14

What is sulphur needed for?

Some amino acids
Some carbs
Biotin
Thiamine

15

What is the reduced form of carbon?

CH4 (Methane)- Organic matter

16

What is the oxidized form of carbon?

CO2 and CO

17

What does CO2 fixation involve?

The conversion of CO2 into organic matter

18

What type of organism would perform CO2 fixation?

Autotrophs (chemolithotrophy)

19

What carries out nitrogen fixation?

Archae
Ex: Rhizobium

20

Assimilatory reduction

Cytoplasmic
Not coupled to electron transport
Repressed by O2

21

Dissimilatory reduction

Membrane bound
Coupled to electron transport
Repressed by ammonia

22

What is the relationship between the carbon and nitrogen cycles?

They are coupled

23

Prototrophic

Can make their own cofactors for enzymes

24

Group translocation

Solute is modified as it is transported

25

What molecule assists in iron uptake?

Siderophore

26

Defined media

All components and amounts known
Simple uses only 1 carbon source

27

Complex media

Specific amounts and composition not known
Usually contains digests of other organisms
Many are supportive media (allows growth of wide range of organisms)

28

Enriched media

Starts as complex, then other components added (ex: blood), for fastidious microbes

29

Selective media

Allows growth of some
Inhibits others

30

Differential media

Allows for ID of bacteria based on colours, growth, or appearance of colonies

31

Ex of differential media

Eosin methylene blue agar
-Identified lactose fermentors

32

What types of media is blood agar?

Enriched
Differential

33

EMB agar is...

Selective
Differential

34

Blood agar identified pathogens based on...

Hemolysis

35

Blood agar- Alpha

Green zone around colonies that signify incomplete hemolysis

36

Blood agar- Beta

Clear zone of complete hemolysis within a yellow colony

37

Blood agar- Gamma

No hemolysis (Clear)

38

How do you typically isolate a pure culture?

From stock solution
Dilute
Plate
Choose well-isolated colony
Replate

39

What are some features of ancient cells?

Some lack PTG wall
Must be osmotically protected
Do not divide by binary fission or use cytoskeletal proteins

40

What are all bacteria and archaea in regards to their genome?

Haploid

41

What are some points of binary fission?

Can be symmetrical- not always
May involve formation of septum

42

What are the steps of binary fission?

Elongation
Septum formation
Cell separation

43

What are the 2 main points in the bacterial cell cycle?

1. Replication and partitioning of DNA
2. Cytokinesis

44

What direction is DNA replication in bacteria?

Bidirectional

45

5 steps of cytokinesis

1. Site selection
2. Assembly of FtsZ ring
3. Linkage of FtsZ ring to membrane
4. Assembly of synthesis apparatus
5. Constriction of cell, septum formation

46

What is FtsZ similar to in a eukaryotic cell?

Tubulin- Forms a ring that results in separation

47

What forms the divisome?

Fts proteins

48

What forms the ring?

FtsZ

49

What is FtsA similar to?

Actin (hydrolyzes ATP)

50

What anchors the ring to the membrane?

ZipA anchor

51

What do the min proteins do? (MinB)

Align the FtsZ ring

52

What is MreB similar to? What does it do?

Actin- Forms the helical simple cytoskeleton in bacteria and archaea

53

What is the region of new growth of the PTG layer called?

Divisome

54

What are 3 other forms of reproduction?

Budding
Spore formation
Baocyte formation (endospore)

55

Exponential growth

Number of cells doubles in a constant time interval

56

Generational time

g= t/n
Duration of exponential growth divided by the number of generations

57

Division rate

v= 1/g
Growth rate is another way to describe the division rate: Doubles per unit time

58

What are the 4 phases of the growth curve?

Lag
Exponential
Stationary
Death

59

What phase would you normally perform experiments on these cells?

Exponential

60

Batch culture

A closed system

61

Continuous culture

Open system; replenish nutrients, remove waste, will eventually reach equilibrium

62

What does nutrient concentration affect in a culture?

Growth and yield

63

What are direct counts for measuring growth?

Use a counting chamber (hemocytometer)
Each chamber has a known volume- Count the cells and find the concentration (use a stain for viable cell counts)

64

What is flow cytometry?

Cells are fluorescently stained and then founded by their fluorescence- Can be used to sort too (FACS)

65

Coulter counter

Based on electrical flow

66

What is a disadvantage of plate counting?

Time- have to culture

67

What is optical density?

The light is being bounced off particles and measured

68

What are some disadvantages of OD counting?

Dead matter
Differing cell sizes
Only accurate over a narrow range

69

What are advantages of dry weight and OD readings for cell counts?

Simple, cheap, and fast, but they are an estimate

70

What are the 3 types of cardinal temperatures?

Minimum, maximum, and optimum

71

What effects where the cardinal temperature ranges lay for an organism environmentally?

Media and nutrient content

72

What happens at minimum temperature?

Membrane is gelling
Transport is too slow to sustain life

73

What happens at maximum temperature?

Protein denaturation and collapse of membrane- Thermal lysis

74

What temp do enzyme catalytic rates double at?

10 degrees celsius

75

Psychrophile

Prefer colder temperatures

76

Mesophile

Prefer moderate temperatures (human body temp)

77

Thermophile

High temperatures (above 45)

78

Hyperthermophile

Prefer VERY high temperatures (above 80)

79

What class are hyperthermophile?

Archae
Can survive autoclaves

80

Psychotrophs

Can grow at low, but prefer higher

81

What is the lowest temperature microbes survive at?

-12 degrees
-Psychromonas

82

What are some adaptations for cold temperatures?

Cold shock proteins and cryoprotectants

83

What are some adaptations for warm temps?

Heat stable proteins
Special solutes in cytosol

84

What is pH?

-log [H+]

85

What are the 3 classes of external pH dwelling microbes?

Neutrophiles
Acidophiles
Alkalophiles

86

Neutrophiles

(5.5-7.9), most bacteria and protists

87

Acidophiles

(0-5.5), most fungi

88

Alkalophiles

(>8), most marine organisms

89

What is the internal pH range for all classes?

Cannot drop below 5, and is usually around 7

90

How do acidophiles stay neutral?

Transport cations into the cell, pump out H, highly permeable membranes

91

How do alkalophiles stay neutral?

Use Na instead of H to fuel transport

92

What is water activity (aw)?

Ratio of vapour pressure of air in eq with a solution to the vapour pressure of pure H2O

93

What is the aw of water?

1.0000

94

Halotolerant

0-5% salinity

95

Halophile

4-8% salinity

96

Extreme halophile

>15%- Actually require this amount of salt

97

Osmophiles

Live in high concentration of sugars

98

What are some adaptations for high solute concentration environments?

Mechanosensitive channels
Compatible solutes (sugars, OHs, AAs)

99

Where do aerobes grow?

The surface

100

Where do anaerobes grow?

Away from the surface

101

Where do facultative anaerobes grow?

Throughout media, but prefer the surface

102

Where do microaerophiles grow?

Just below the surface

103

Where do aerotolerant anaerobes grow?

Throughout, without any preference

104

What is ROS?

Reactive Oxygen Species- damages cells

105

What is ROS a byproduct of?

Respiration

106

How do cell combat ROS?

Have enzymes that break down ROS

107

Barotolerant

Can survive at high pressure

108

Piezophillic

Only survives at high pressure

109

How do microbes survive at high pressure?

Increased unsaturated fatty acids

110

What is a biofilm?

Non-motile extracellular polymeric substance, many species of bacteria and adherent to surfaces

111

What percentage of all bacteria live on biofilms?

80%

112

What are some pros of living in a biofilm?

Recycling of nutrients
Protection from stress
Biodiversity facilitated gene pool
Large gene pool

113

What are the 4 stages of a biofilm formation?

1. Attachment
2. Colonization
3. Development
4. Active dispersal

114

Biocide

A chemical or physical agent that inactivates microbes- broad spectrum

115

Sterilization

All cells, spores, and acellular entities destroyed or removed

116

Disinfection

Killing or severely inhibiting growth of microbes that may cause disease (surfaces/inanimate objects)

117

Decontamination

Treatment of an object making it safe to handle

118

Sanitization

Related to disinfection- level of microbes deemed safe by public health standards

119

Antiseptic

Chemical agent that kills or inhibits pathogenic microbes on tissues (generally not toxic)

120

Chemotherapy

Use of chemical agent to kill microbes within the host tissue

121

Decimal reduction time

Time required to kill 90% of microbes (one log cycle)

122

What is UV radiation good for?

Low amount of penetration- good for air and exposed surface and water

123

Where would we see UV radiation in use?

Meat packing
Biohazard cabinets
Water treatment

124

What is ionizing radiation good for?

Deep penetration
Destroys spores- Not good at killing viruses, good for dry foods

125

Depth filter

Fibrous material in a think layer with small channels

126

2 types of depth filter

Berkfield (diatoms)
Chamberland (unglazed porcelain)

127

Membrane filter

Porous
Made with a variety of material of different pore sizes

128

HEPA filters

High efficiency particulate air filter- made of fibreglass, 0.3 um retention
Can filter out bacteria and viruses

129

Nucleopore filters

Made from polycarbonate, uniform in pore size - used for prepping samples in SEM

130

How does triclosan work?

Inhibits production of fatty acids - toxic to aquatic animals, hormone issues in rats

131

What does alcohol work against?

Bacteriacide and fungicide, does not kill spores

132

What is the best % to use in alcohol?

75%- if higher it causes shrinkage of the membrane and makes it hard to kill.
95% is used for flame sterile

133

How do phenolics work?

Denatures proteins, disrupts membranes

134

Why are phenolics so useful?

Remain active on surfaces for long periods, can kill mycobacteria (tuberculosis)

135

What do halogens work as?

Disinfectants and antiseptics

136

What is iodophore?

Water soluble iodine with organic component - releases iodine slowly to reduce irritation - used in hospitals to prep skin

137

What is silver nitrate used for?

Drops in newborns' eyes to reduce chance of infection

138

What is copper sulfate used for?

Preventing algal growth

139

What are quaternary ammonium compounds?

Detergents - good for skin and utensils, work well with phenolics, but not good in presence of organics

140

What do aldehydes act as?

Sporicides - Highly toxic and reactive

141

Why would you use sterilizing gas?

Good for sterilizing materials that cannot be heated

142

What is the difference between bacteriostatic and bactericidal?

Bacteriostatic- Stops growth, but doesn't kill (if you remove the agent, they will continue to grow)
Bactericidal- Will kill off cells, but won't get rid of the debris

143

What is MIC? How is it determined?

Minimum inhibitory concentration
Dilution test

144

Diffusion test

Inoculate solid media
Add disks soaked in different bactericide
See which ones inhibit growth

145

Phenol coefficient test

Similar to dilution test, but compare the results to the efficacy of phenols

146

Catabolism

Breaking down material

147

Anabolism

Building large macromolecules from small precursors

148

Chemical work

Synthesizing molecules (anabolism)

149

Transport work

In/out of cell, or within- bacteria rely only on Brownian motion, whereas eukaryotes need energy input

150

Mechanical work

Movement- Convert chemical energy to physical energy

151

What is free energy and what does it do?

It is the energy available to do work, and it drives all reactions in the cell

152

What are conditions for the standard free energy?

pH of 7, 25 degrees, 1 atm pressure, 1M conc. of products and reactants

153

What does a negative free energy mean?

Exergonic - occurs spontaneously

154

What does a positive free energy mean?

Endergonic - does not occur spontaneously

155

How do you calculate standard free energy?

-RTlnKeq

156

What does G=0 mean?

The reaction is in equilibrium

157

What does the free energy under cellular conditions depend on?

Only on the G of reactants and products- provides no info on the rate of reaction

158

How do you calculate the free energy?

Standard free E + RTln (conc. products) / (conc. reactants)

159

How does ATP get used to drive reactions?

It conserves energy from exergonic reactions and this energy can then be used to drive endergonic reactions

160

What are metabolic pathways catalyzed by?

Enzymes and ribozymes

161

Why are redox reactions important?

They conserve energy

162

When you hydrolyze ATP what do you get?

ADP and orthophosphate (inorganic phosphate) + (-30.5 kJ/mol of energy)

163

What type of bond is very high energy?

Anhydride

164

What type of bond is very low energy?

Ester

165

How do enzymes increase reaction rate?

Stabilize transition state and lower activation energy

166

What do enzymes not change in terms of a reaction?

The free energy or the equilibrium constant

167

Who proposed the lock and key model?

Emil Fisher, 1890

168

Who proposed the induced fit model?

Daniel Koshland, 1958

169

What is methotrexate?

First chemo drug- a competitive inhibitor

170

How does penicillin work?

Suicide inhibitor for glycopeptide transpeptidase - does not allow cross linking of the PTG layer

171

What are the 3 methods of regulation of metabolism?

Metabolic channeling, amount of enzyme, enzyme effectors

172

What is metabolic channeling?

Compartmentalize substrates, or have them in a gradient

173

Why does feedback inhibition target the first step of a signal transduction or branch point?

Efficient, less wasteful (no intermediates), don't spend any more energy than needed

174

What is an allosteric enzyme?

The active site is separate from the regulatory site

175

What is allosteric regulation?

End product has different shape than starting product; can be used as a regulatory device for when the concentration of product becomes too high - the product can then bind to the regulatory site and inhibit the enzyme from reacting

176

Reducing agent

Electron donor

177

Oxidizing agent

Electron acceptor

178

Standard reduction potential (Eo)

The equilibrium constant that measures the tendency for the donor to lose electrons under standard conditions

179

How do we relate reduction potentials to standard free electrons?

Standard free E = -nF(standard reduction potential)

180

When looking at a redox tower, where are the oxidized and reduced forms?

Reduced on right, oxidized on left

181

If we have negative Eo, where does the equilibrium favour?

The oxidant

182

If we have a positive Eo, where does the equilibrium favour?

The reductant