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Biol 371 > CMMB 343 > Flashcards

CMMB 343 Flashcards

1
Q

What it the largest known prokaryote?

A

Thiomargarita

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2
Q

Who was the father of microbiology?

A

Anton van Leeuwenhoek

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3
Q

What is bioremediation?

A

Using bacteria to clean up toxic compounds

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4
Q

What are the two classifications for carbon acquisition?

A

Heterotrophs - use multiple compounds as a carbon source

Autotrophs - use CO2 as the main source (usually primary producers)

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5
Q

What are the three ways in which organisms gain their energy?

A

Chemolithotrophy
Chemoorganotrophy
Phototrophy

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6
Q

In chemolithotrophs what do they use as an energy source?

A

Inorganic chemicals like H, H2S, Fe, NH4 etc

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7
Q

In chemoorganotrophs what do they use as an energy source?

A

Organic chemicals like glucose, acetate etc.

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8
Q

Who was the father of taxonomy?

A

Carolus Linnaeus

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9
Q

What did Ernst Heckel’ propose the kingdom tree should look like?

A
  • Would have three groups
  • Is not based on empirical data
  • The organisms always evolve to a higher more complex state
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10
Q

Who suggested the use of DNA to form the tree?

A

Carl Woese

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11
Q

What were 3 reasons why the 16S rRNA was a good fit for testing the tree of life?

A
  • it is universal to all organisms
  • does not undergo lateral transfer between different species
  • mutates very slowly
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12
Q

Which domain is most closely related to archaea?

A

Eukarya

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13
Q

What species is the largest group of bacteria?

A

Proteobacteria

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14
Q

What are the two phylum of Archaea?

A
  • Crenarchaeota

- Eurarchaeota

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15
Q

How to identify the Crenarchaeota

A
  • usually very thermophilic (116C)

- many are lithotrophic on S or H

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16
Q

How to identify the Euryarchaeota

A
  • includes the methanogens and the extreme halophiles
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17
Q

How do E. coli obtain their energy?

A

Chemoorganotrophic

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18
Q

What are three common soil bacteria in Proteobacteria?

A
  • Pseudomonas
  • Azotobacter
  • Rhizobium
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19
Q

What is a photoautotrophic proteobacteria?

A

Purple sulfur bacterium (chromatium).

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20
Q

Chromatium do not use photosynthesis. What do they use instead?

A

They don’t use photosynthesis since they do not use O2 as a final electron acceptor they use H2S instead.

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21
Q

Which species is dominant in microbial mats?

A

Green nonsulfur bacteria (Chloroflexus)

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22
Q

The gram positive group has 5 different classifications under it. What are they?

A
  • spore formers (Bacillus, Clostridium)
  • antibiotic producing (Streptomyces)
  • lactic acid producers (Lactobacillus and Streptococcus)
  • mycoplasmas (lack a cell wall)
  • plant symbionts
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23
Q

Classify Firmicutes.

A

Gram positive endospore formers

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24
Q

What are actinobacteria?

A

Gram positive that produce antibiotics

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25
Q

Plantomycetes and Spirochaetes have unique morphologies. What are they?

A

Plantomycetes - stalked bacteria

Spirochaetes - helical bacteria

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26
Q

What is special about Deinococcus?

A

They have unusual cell walls and are highly resistant to radiation.

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27
Q

What term did Ferdinand Cohn coin?

A

Bacteria meaning small rod or staff and grouped the organisms based on shape.

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28
Q

What is DNA hybridization?

A

Mixing of two genomes to compare similarities

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29
Q

How much must the DNA match to be considered the same species through hybridization?

A

More that 70% must match

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30
Q

When comparing the 16S rRNA, how different do they need to be to be considered a new species?

A

1-3% different

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31
Q

Which do you test first; DNA hybrid or 16S rRNA?

A

rRNA

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32
Q

What does ICSP stand for?

A

International Committee on Systematics of prokaryotes

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33
Q

Who regulates the naming of bacteria?

A

International Code of Nomenclature of Bacteria

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34
Q

What are extremophiles?

A

Bacteria that prefer conditions outside of the normal

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35
Q

What constitutes the largest group of extremophiles?

A

The archaea

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36
Q

Define psychro-

A

cold temperatures

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37
Q

Define thermo-

A

high temperatures

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38
Q

Define meso-

A

middle

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39
Q

Define alkali-

A

high pH

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40
Q

Define piezo-

A

high pressure

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41
Q

Define xero-

A

dry

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42
Q

Define radio-

A

radiation

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43
Q

define -troph

A

average or some ability

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44
Q

define facultative

A

sometimes they can/can’t

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45
Q

Give examples of thermophilic habitats

A
  • deserts
  • compost, decaying matter
  • deep biosphere
  • geothermal systems
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46
Q

What are three ways methods for surviving high temperatures?

A

1- strong bonds to stabilize proteins to prevent denaturation
2- decrease membrane fluidity
3- increase RNA stability by increasing GC content

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47
Q

How do bacteria prevent proteins from denaturing?

A
  • certain amino acids provide more heat tolerant folds
  • more ionic bonds between basic and acidic amino acids
  • production of solutes
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48
Q

Name a sulfide/sulfur oxidiser

A

Thiothrix

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49
Q

Name three archaea that are hyperthermophile (>80C) that are also hydrogen or sulfur-metabolisers

A
  • Pyrodictium
  • Pyrolobus
  • Sulfolobus
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50
Q

What do methanogens produce?

A

Methane gas

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51
Q

What is the range of a neutrophile?

A

6-8

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52
Q

Who is the champion acidophile?

A

Ferroplasma acidarmanus at a pH of 0

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53
Q

What is the problem with acidophile/alkylophile?

A

The membrane must be impermeable to protons and so it is difficult to maintain a proton motive force (some use sodium)

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54
Q

Which bacteria is highly radiation resistant?

A

Deinococcus radiodurans 1000x more than humans

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55
Q

How does Deinococcus radiodurans protect their chromosome?

A
  • tight coils
  • repair damaged DNA
  • 4 copies of chromosomes but only 2 are active at a time
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56
Q

What are endospores?

A

Differentiated cells that are highly resistant. Only found in some gram positive cells

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57
Q

What does an endospore germinate into?

A

a vegetative cell

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58
Q

What are clorosomes?

A

They are light antennae that allow the cell to grow under low light

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59
Q

What are two bacteria that use clorosomes?

A

Chloroflexi and Chlorobi

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60
Q

What are carboxysomes?

A

they are special structures that house calvin cycle enzymes like RubisCO-

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61
Q

What cells are purple and what cells are red in a gram stain?

A 
Purple= positive
Red= negative
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62
Q

What are the three components of a gram positive membrane?

A
  • cytoplasmic membrane
  • peptidoglycan
  • teichoic acids
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63
Q

What are the four components of the gram negative bacteria?

A
  • cytoplasmic membrane
  • peptidoglycan
  • periplasm
  • outer membrane
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64
Q

What is the cytoplasmic membrane consist of?

A

Phospholipid bilayer

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65
Q

What makes up the outer membrane in gram negative bacteria?

A
  • lipopolysaccharide

- protein

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66
Q

What are used to strengthen the cytoplasmic membrane?

A
  • sterols
  • hopanoids
  • saturated
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67
Q

What are 4 roles of membrane proteins?

A
  • transport
  • environmental sensing (signal transduction, chemotaxis)
  • electron transport
  • membrane and cell wall assembly
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68
Q

What is peptidoglycan made of?

A

N-acetylglucosamine and N-acetylmuamic acid. M binds to another M through glycosidic bonds. M and G alternate.

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69
Q

What are two agents that break down peptidoglycan?

A

Lysozyme - tears in egg white

Penicillin

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70
Q

How does lysozyme break down peptidoglycan?

A

Hydrolyses peptidoglycan

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71
Q

How does penicillin break down peptidoglycan?

A

Inhibits cross linking of the glycan strands. (inhibits transpeptidation)

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72
Q

What is the function of teichoic acid in gram positive bacteria?

A
  • maintain porosity of cell wall
  • anchor cell wall to cell membrane
  • cell shape
  • capture cations
  • regulate cell wall turnover
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73
Q

What does growth mean?

A

An increase in the number of cells

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74
Q

What is binary fission?

A

Cell elongation

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75
Q

what is generation time?

A

time required for a population of microbial cells to double

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76
Q

What allows a cell to divide?

A

FtsZ - Filamentous Temperature Sensitive

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77
Q

Who has FtsZ?

A

All bacteria

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78
Q

How does FtsZ work?

A

Creates a ring (Z-ring) in a GTP dependent maner and then constricts

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79
Q

What connects the FtsZ ring to the cytoplasmic membrane?

A

ZipA

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80
Q

What does FtsA do?

A

Helps connect FtsZ to the membrane and recruits other proteins related to actin

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81
Q

What does FtsK do?

A

Mediates the separation of chromosomes to daughter cells

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82
Q

What is MreB?

A

This determines the shape of the cell. Not found in coccus cells

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83
Q

How does MreB work?

A

Forms spiral bands, where the bands meet the membrane they stimulate growth

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84
Q

What are autolysins?

A

Hydrolyze the M G glycosidic bonds of peptidoglycan backbone

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85
Q

What does transpeptidation do?

A

Forms the peptide cross links between M residues

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86
Q

What are the 4 growth phases?

A

1 lag
2 exponential
3 stationary
4 death

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87
Q

What is a chemostat?

A

an open, continuous flow system where growth rate is controlled by the availability of a single nutrient. Allows for constant growth rates

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88
Q

What is washout?

A

Washout is when the dilution rate is greater than the growth rate.

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89
Q

How to calculate the dilution rate (D)?

A

D=F/V
F= flow rate (mL/h)
V= vessel volume (mL)

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90
Q

What happens when the dilution rate increases at low dilution rates?

A

Both cell density and growth rate increase. More nutrients available for reproduction

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91
Q

What is metabolism?

A

The sum total of all chemical reactions that occur in a cell

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92
Q

When is deltaG exergonic?

A

negative

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93
Q

What is the deltaG of fumarate to succinate?

A

-86 kJ

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94
Q

What is the deltaG of NO3 to NO2

A

-163 kJ

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95
Q

What is the deltaG of O2 to H2O?

A

-237 kJ

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96
Q

What is substrate level phosphorylation?

A

Phosphate from organic group added to ADP

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97
Q

What is oxidative phosphorylation?

A

Making of ATP in the electron transport chain.

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98
Q

What is the net products made in glycolysis?

A

2 pyruvate
2 ATP
2 NADH

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99
Q

Which is more efficient? production of ethanol or lactate?

A

Lactate (32% vs 27%)

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100
Q

How many ATP are formed during aerobic respiration?

A

38

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101
Q

What does the proton motive force do?

A
  • Drive ATP synthase
  • flagellar motor
  • transport systems
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102
Q

What is denitrification?

A

Anaerobic respiration that uses nitrate (NO3) as an electron acceptor (NO3->N2)

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103
Q

What is good about iron oxidizing?

A

Acidophilic bacteria useful in concentration of copper ore

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104
Q

What is bad about iron oxidizing?

A

Can release sulfuric acid

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105
Q

What is nitrogen fixing?

A

Nitrogen gas to ammonia

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106
Q

What is nitrification?

A

Ammonia to nitrate (NO3). This happens in two steps
NH4 -> NO2 nitrosification,
NO2 -> NO3 nitrification

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107
Q

What is annamox?

A

The anaerobic oxidation of ammonia to nitrogen gas

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108
Q

What are the two bacteria involved in nitrification?

A

Nitrosomonas and Nitrobacter

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109
Q

What bacteria use denitrification?

A
  • bacillus
  • paracoccus
  • pseudomonas
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110
Q

What bacteria use free-living, aerobic nitrogen fixing?

A

Azobacter
Cyanobacteria
Alcaligenes

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111
Q

What bacteria use free-living, anaerobic nitrogen fixing?

A

Clostridium
Rhodospirillum
Methanococcus
purple and green bacteria

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112
Q

What bacteria use annamox?

A

Brocadia

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113
Q

What is the relationship between symbiotic N2 fixers?

A
  • plant produces anaeroic environment
  • plant supplies nutrients
  • bacteria supply ammonia
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114
Q

What enzyme do bacteria use during nitrogen fixing?

A

Nitrogenase

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115
Q

How do azobacter protect the nitrogenase?

A

respire oxygen at cell surface so the cell remains anaerobic

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116
Q

How do cyanobacteria protect nitrogenase?

A

they fix nitrogen in a heterycyst - a cell in the chain

117
Q

How do clostridium protect nitrogenase?

A

inhabit oxygen free environment

118
Q

Why is nitrate (NO2) low in soil?

A
  • plants use it readily

- it is leached out

119
Q

What are methane hydrates?

A

frozen methane

120
Q

What is the most transferred carbon reservoir?

A

atmosphere

121
Q

What does the calvin cycle do?

A

Fixes CO2 to make sugar

122
Q

How much ATP is used to make one sugar?

A

18

123
Q

What is methanogenesis?

A

reduction of CO2 to CH4

124
Q

What is syntrophy?

A

Eating together

125
Q

What is symbiosis?

A

Living together

126
Q

What do syntrophs do?

A
  • secondary fermentors use acetate from primary fermentors (team up with methanogens)
127
Q

Define species richness

A

the total number of different species present

128
Q

Define species abundance

A

the proportion of each species in an ecosystem

129
Q

What are biofilms?

A

group of bacteria that adhered to a surface and are enclosed in a matrix by the cells that is usually made of polysaccharides.

130
Q

Why would cells form biofilms?

A
  • self defense
  • stay in favourable niche
  • live in close association
131
Q

What are microbial mats?

A

Very thick biofilms

132
Q

What are the two main classes of soil?

A
  • Mineral

- Organic

133
Q

What are the 4 levels of soil in order?

A
  • O horizon
  • A horizon
  • B horizon
  • C horizon
134
Q

What is the defining feature of o horizon?

A

Undecomposed matter

135
Q

What is the defining feature of a horizon

A

lots of organic matter and so lots of growth of plants and cells

136
Q

What is the defining feature of b horizon?

A

subsoil, humus

137
Q

What is the defining feature of c horizon?

A

soil base any minerals are from rock

138
Q

What is the most abundant marine heterotroph?

A

Pelagibacter

139
Q

What is an oligotroph?

A

organism that grows best at low nutrient concentrations

140
Q

What is proteorhodopsin?

A

allows cells like Pelagibacter to use light energy to drive ATP synthesis

141
Q

What type of energy using bacteria are found in vents?

A

chemolithotrophic

142
Q

Define parasitic

A

the microbe benefits at some expense to the host

143
Q

Define pathogenic

A

the microbe causes a disease in the host

144
Q

Define commensal

A

the microbe has no discernible impact on the host

145
Q

Define mutualistic

A

the microbe is beneficial to the host

146
Q

What do fungus and alga or cyanobacterium make?

A

lichens

147
Q

What is the relationship on lichens?

A
  • alga is photosynthetic and make organic matter
  • lichen acids dissolve rock releasing minerals
  • fungus protects the microbe from dessication
148
Q

What is Chlorochromatium aggregatum?

A

not a real name just a consortium between non-motile green sulfur and a motile non-phototrophic bacteria

149
Q

What is the rhizosphere?

A

the region immediately outside the root

150
Q

What is a phyllosphere?

A

surface of the plant leaf

151
Q

Give an example of a legume

A
  • soybean
  • clover
  • alfalfa
  • beans
  • peas
152
Q

What is the role of nod factors?

A

Induce root hair curling

153
Q

What are symbiosomes?

A

When rhizobia cells multiply in the plant it becomes swollen and mishaped and is called bacteroids. then the plant surrounds the bacteroids

154
Q

What is leghemoglobin ?

A

a molecule capable of binding to oxygen

155
Q

What is the bacterial genome?

A

all chromosomes and plasmids

156
Q

Do plasmids carry essential genes?

A

No

157
Q

When can plasmids replicate?

A

Any time during the cell cycle

158
Q

What are the three periods in cell replication?

A
  1. B period - birth
  2. C period - replication (constant based on species)
  3. D period - division
159
Q

Which from of DNA is prominent and why?

A

Circular because;

  • smaller
  • less complication DNA replication
  • resistance to exonnucleases
160
Q

In which direction is DNA replicated?

A

5’ -> 3’

161
Q

What is the size of E coli genome?

A

4.6 x 10^6 bp

162
Q

What is an advantage to having a divided genome?

A

Less time to replicate

163
Q

What are two consequences for bacteria being haploid?

A
  • mutation will have immediate consequence

- allows genes to be turned on/off

164
Q

How does HU binding protein work?

A

The Heat Unstable protein had an N-terminal and a C-terminal. C-terminal is a flexible arm for binding DNA

165
Q

What enzyme supercoils DNA?

A

gyrase

166
Q

What are operons?

A

Genes that are grouped together as they have related functions

167
Q

Why is replication and translation done in the same direction?

A

If they were done in opposite directions it would result in head on collision and slow both processes

168
Q

On average, how many base pairs per gene?

A

1 kb

169
Q

What mediates protein splicing?

A

Self catalyzed by intein

170
Q

Do all domains have inteins?

A

Yes

171
Q

How does a cell turn on the promoter of Tn10?

A

must remove methylation

172
Q

What are three ways to decrease the frequency of transposition?

A
  1. only have a few promoters
  2. have inactive promoters
  3. only allow for a small window of time for this to occur
173
Q

There are 6 requirements for the transposition process

A
  1. DNA homology between TE and target site not required
  2. Tnp encoded by TE mediates the transposition process (RecA independent)
  3. Tnp recognizes a short target sequence
  4. After transposition target sequence is duplicated forming a direct repeat
  5. Tnp recognizes the inverted repeat at the end of the TE
  6. insertion sites may or may not be random
174
Q

Which TE are non-random?

A

Tn7 (ABCD) and Tn10

175
Q

Which TE are random?

A

Mu, Tn5 and Tn7 (ABCE)

176
Q

What does TnpA/B do?

A

recognize IR

177
Q

What does TnpC do?

A

Connector or activator of tnp

178
Q

What do TnpD/E do?

A

target site selection

179
Q

What are the 2 classes of transposable elements?

A
  1. Insertion sequences (IS)

2. Transposons

180
Q

What must be present for an insertion sequence to move?

A
  • must have transposase encoded

- must be flanked by inverted repeats

181
Q

What are the 2 types of transposons?

A
  1. composite

2. complex

182
Q

Give an example of a composite transposon

A

Tn5 (kan str bleo)

183
Q

What is unique about composite transposon?

A

they transfer genes between two IS

184
Q

What is an autonomous transposon?

A

Capable of moving on their own as they have tnp encoded

185
Q

What is unique about complex transposons?

A
  • not based on IS

- transfer additional information

186
Q

Give an example of a complex transposon

A

Tn3, Tn7

187
Q

What is conservative transpositions?

A

the TE moves from one site to another and results in only 1 copy
ex. Tn5, Tn7

188
Q

What is replicative transposition?

A

the TE copies in one site and inserts into another resulting in 2 copies
ex. Mu, Tn3

189
Q

What must be present to have replicative transposition?

A

Resolvase

190
Q

What are the consequences to TE?

A
  1. Gene inactivation (insertional mutagenesis)
  2. Turn on repressed genes
  3. deletion via recombination
  4. inversion via recombination
  5. polar effect
  6. gene translocation
191
Q

What is the polar effect?

A

disruption of the first gene in an operon results in inactivation of downstream genes. The TE carries a transcription factor causing mRNA to prematurely terminate

192
Q

How do plasmids replicate?

A

self replication

193
Q

what are the different types of plasmids?

A

F -fertility
R
M - metabolism
Col - colicin (kills neighbor cell)

194
Q

What are the most common forms of plasmids?

A

circular, double stranded

195
Q

What genes are important in plasmids?

A
  • ori : replication origin
  • Rep : replication protein
  • ABr : antibiotic resistance
196
Q

What does Rep do in Theta mode?

A

recognizes ori and unwinds

197
Q

What does Rep do in rolling circle mode?

A

recognizes ori and nicks

198
Q

Give an example of a narrow host range

A

pBR322 only replicates in E coli

199
Q

Give an example of broad host range

A

RK2 - gram negative

RSF101 - both gram - and +

200
Q

The F plasmid has two specific genes, what are they?

A

CcdB (Controlled Cell Death)

CcdA (antidote to CcB)

201
Q

What are the 3 methods to horizontal transfer?

A
  1. conjugation
  2. transformation
  3. transduction
202
Q

What are two types of plasmids for conjugation?

A
  1. self-transmissible

2. Mobilizable

203
Q

Self transmissible requires two genes, what are they?

A
  1. dtr (DNA Transfer and Replication)

2. mpf (mating Pair Formation)

204
Q

Mobilizable only requires 1 gene. What is it?

A

mpf - mating pair formation

205
Q

What does Hfr stand for?

A

High Frequency Recombination

ex IS3

206
Q

What is a suicide vector?

A

Can only replicate in E coli and so after conjugation the plasmid will not replicate in the host.

207
Q

What is good about transformation?

A

it is fast acquisition of new genes

208
Q

What are the 2 types of transformation?

A
  1. natural

2. Artificial

209
Q

Which bacteria are non-specific?

A

Streptococcus pneumoniae
bacillus subtilis
Helicobacter pyroli

210
Q

Which bacteria are specific?

A 
Haemophilus influenzae (5' AAGTGCGGT 3')
Neisseria gonorrhoeae (GCCGTCTCAA)
211
Q

What are the two ways to make cells competent?

A
  1. chemical
  2. electrical

ex B subtilis become competent when the nutrients run out or high cell density during the early stationary phase

212
Q

What are the 4 steps of DNA transformation in B subtilis and Streptococcus?

A
  1. DNA binding (50 B, 10 S)
    - reversible
  2. Fragmentation
  3. DNA uptake (ATP dependent)
    - ds, no seq specificity
    - as it enters cell the 5’ end is degraded Strop
  4. Recombination
213
Q

What are the steps in transformation in Haemophilus?

A
  1. competence developed in early stationary phase
  2. makes transformase
  3. must have AAGTGCGGT sequences
  4. DNA uptake and recombination
214
Q

What is the chemical method?

A

Use calcium to put pores in membrane during the mid log phase

215
Q

How must the DNA be to be taken in?

A

Circular ds or ss. Linear gets degraded

216
Q

Which is more effective chemical or electroporation?

A

electroporation (90%) vs chemical (10%)

217
Q

What is special about Agrobacterium tumefaciens?

A

It is a pathogen to plants - induces tumor Crown gall

218
Q

How does the bacteria attach to the plant cell?

A
  • plant has pectin

- bacteria has acidic acetylated capsular polysaccharide and cellulose fibril

219
Q

What specifically induces the tumor?

A

Ti plasmid

220
Q

Ti plasmid has 2 genes, what are they?

A

Oncogenes
- growth hormone
- hormone sensitizer
opines

221
Q

What are the three basic forms of viruses?

A
  1. Helical
  2. Polyhedral
  3. Complex
222
Q

In what 2 states do viruses live in?

A
  1. Intracellular state in infected host

2. Extracellular state in virion form

223
Q

What is a capsomere?

A

Assemblage of subunits of the virus capsid

224
Q

What viruses use the helical form?

A
  • M13 phage
  • rabies
  • plant TMV
225
Q

What virus uses complex form?

A

T4

226
Q

What are the 2 steps in viral multipication?

A
  1. Attachment

2. Penetration

227
Q

What is a T4 long tail fiber made of?

A

LPS

228
Q

What is a T4 tail pin (STF) made of?

A

LPS/OmpC

229
Q

What is MS2 and M13 for?

A

conjugation pili

230
Q

How do phage and virus differ in the penetration stage?

A

phage use DNA injection

Virus use entry and uncoating (ex influenze o6)

231
Q

What are the 4 regions of the T4 needle?

A
  • gp27
  • gp5 connector domain (N)
  • gp5 lysozyme domain
  • gp5 helical domain (C)
232
Q

What are the 6 steps to phage invasion?

A
  1. long tail fiber attach (reversible)
  2. short tail fiber attach (irreversible)
  3. DNA releases into tail tube
  4. Sheath contraction -> rotation of tail tube -> screw and punch actions
  5. tail tube penetrates outer membrane and lysozyme digests small opening in peptidoglygan
  6. DNA ejection
233
Q

What are two methods that T4 use for DNA ejection?

A
  1. internal pressure

2. Proton gradient

234
Q

What are two different types of tail?

A

Contractile Ex. T2, T4, Mu

Non-contractile
Long Ex. Lambda, T1, T5
Short Ex. T7

235
Q

Why does T4 DNA have direct repeat at each end?

A

Allows the DNA to become circular after being placed into the host

236
Q

What does burst size mean?

A

How many phage are released for every infected cell

T4 is 200

237
Q

What does DNase do?

A

Consists of DenA and DenB that cut only cytosine containing DNA

238
Q

What does T4 Unf do?

A
  • unfolds the nucleoid (C containing DNA)

- blocks transcription of host DNA

239
Q

How do the phage obtain nucleotides?

A
  • host DNA

- New dNTP biosynthesis

240
Q

What are concatamers?

A

Concatamers are formed when the DNA is replicated and the overhang of one strand bonds with another so as not to lose any DNA

241
Q

What are the 3 units associated with DNA packaging?

A

gp20
gp17 N and C domain
gp16

242
Q

What does gp 20 do?

A

acts as a channel into the phage head

243
Q

What does gp17 do?

A

The N domain ATPase acts as a pump (2bp/ATP) the C domain binds to the DNA and Cleaves it once the head is full

244
Q

What does gp16 do?

A

speeds up ATPase

245
Q

What does H1N1 stand for?

A 
h= hemagglutinin
n= neuraminidase
246
Q

How does Tamiflu work?

A

Inhibits neuraminidase

247
Q

What shape are proteins in for secretion in sec-dependent manor?

A

Unfolded so they will fit through the pores

248
Q

Describe the Twin Arginine Translocation (TAT) requirements

A
  • must have S/TRRXFLK

- sec independent

249
Q

What are two types of proteins that are gram negative specific?

A
  • periplasmic proteins

- outer membrane proteins

250
Q

What are the four components of sec-dependent protein secretion?

A
  1. N-terminal signal sequence
  2. membrane channel
  3. translocase SecA
  4. chaperone proteins (prevent folding)
251
Q

What is the energy source for Sec-dependent protein secretion?

A
  • ATP

- proton gradient

252
Q

Where will peptidase cleave the signal seqence?

A

after ala-x-ala followed by neutral or negative aa

253
Q

What are the two functions of SecB chaperone?

A
  1. keeps protein unfolded

2. targets preproteins to translocase (SecA) on the membrane

254
Q

Does SecA require ATP?

A

Yes, ATP allows SecA to bind with SecY/E/G

255
Q

What is the microbiome on humans?

A

all microorganisms on or in the human body

256
Q

What are considered normal microbial flora?

A

microbes usually found associated with a particular human body

257
Q

What is the core microbiome?

A

microorganisms that are found on the same site on most people throughout life

258
Q

How do the microbiota of the GI tract affect humans?

A
  • early development
  • health
  • predisposition to disease
259
Q

What are the 4 main phylotypes found in humans?

A

Firmucutes
Bacteroidetes
Proteobacteria
Actinobacteria

260
Q

What bacteria group colonise sweat glands and skin?

A

gram positive

261
Q

What bacteria forms dental plaque?

A

Streptococci

262
Q

What area of the respiratory system is colonized?

A

Upper not lower

263
Q

Does the urogenital tract have bacteria?

A

No, if E coli or P mirabilis are present they cause UTI

264
Q

Define septicemia

A

a bloodborn systemic infection

265
Q

define toxicity

A

the ability of an organism to cause disease by means of a preformed toxin that inhibits host cell function or kills host cell

266
Q

define Virulence

A

the relative ability of a pathogen to cause disease

267
Q

What is a pathogen?

A

a disease causing microorganism

268
Q

define opportunistic pathogen

A

an organism that causes disease in the absence of normal host resistance

269
Q

What are virulence factors?

A

Enzymes produced by the pathogen to
- break down or alter host tissue to provide access to nutrients Ex. hyaluronidase
- protect pathogen by interfering with host defense
Ex. coagulase

270
Q

What are exotoxins?

A

proteins released from the pathogen cell as it grows

271
Q

What are three categories of exotoxins?

A
  • cytolytic -> lyse membrane
  • AB toxins -> intercellular poison
  • superantigen toxins -> take over immune system
272
Q

How does Diptheria exotoxin work? (AB)

A

prevents protein synthesis

273
Q

How does botulism work?

A

Prevents the release of acetylcholine that would stimulate muscle contraction

274
Q

How does tetanus toxin work?

A

Prevents the release of glycine in inhibitory interneurons causing muscles to stay contracted

275
Q

What are endotoxins?

A

Toxins that are released upon lysis of bacteria

276
Q

What are three features of the adaptive immune response?

A
  1. specificity
  2. Memory
  3. tolerance
277
Q

How are antigens recognized?

A
  • linear
  • conformational
  • can be just 4-6 aa long
278
Q

How do T cells recognize an antigen?

A

antigen must be bound to MHC (major histocompatibility complex)

279
Q

Where do we find MHC I?

A

on all nucleated cells, this is how our body recognizes our tissues

280
Q

Where do we find MHC II?

A

only on anitgen presenting cells like

  • macrophages
  • b cells
  • dendritic cells
281
Q

How doe MHC I and MHC II differ?

A

MHC II is not limited to the number of amino acids it can bind whereas MHC I can only bind 8 -11 amino acids

282
Q

What do granzymes do?

A

they are a protease that stimulates apoptosis

283
Q

What is positive selection of T cell education?

A

t cells interact with self MHC then proliferate. Takes place in the thymus

284
Q

What is negative selesction of t cell education?

A

t cells are eliminated if they strongly interact with self MHC this takes place in the medullar region

285
Q

What are the three languages of quorum sensing?

A
  • Autoinducer 1
  • short peptides
  • autoinducer 2
286
Q

What are the key components of quorum sensing?

A
  1. signal generation
  2. signal detection
  3. response -> gene activation
287
Q

Where do we find autoinducers?

A

gram negative

288
Q

What is LuxI/LuxR used for?

A

Lux1 makes AI-1 while LuxR senses AI-1

289
Q

How does autoinducer work?

A

receives a chemical signal like serine, homoserne, homoserine lactone, acyl-homoserine lactone

Biol 371 (6 decks)

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