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bisc 333 > final!!! > Flashcards

final!!! Flashcards

1
Q

biological signaling can be broken down into 3 parts:

A

input, signal transduction, output

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2
Q

signaling systems can control many different

A

genes/operons at the same time

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3
Q

the set of genes/operons controlled by a single signaling system is called a

A

regulon

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4
Q

regulons can induce and repress

A

different genes/operons at the same time

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5
Q

anti-sigma factors

A

control sigma factor availability

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6
Q

sigma factors

A

proteins that bind to promoters and control gene expression

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7
Q

promoter

A

region of dna where rna polymerase binds to initiate transcription

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8
Q

ecf sigma factors activated by

A

degradation of the anti-sigma factor

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9
Q

input signal activates

A

protease

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10
Q

protease

A

enzyme that degrades proteins

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11
Q

misfolded proteins

A

stress response

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12
Q

spoll ab

A

anti-sigma factor in bacillus sporulation

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13
Q

spoll aa

A

anti anti-sigma factor in bacillus sporulation

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14
Q

activity of spoll ab is regulated by

A

activity of spoll aa

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15
Q

spoll e

A

protein removes phosphate from spoll ab

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16
Q

spoll aa is inactivated by

A

phosphorylation

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17
Q

sporulation signal induces

A

spoll e to remove P

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18
Q

two component signaling

A

major bacterial signaling mechanism with two protein components: sensor histidine kinase and response regulator

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19
Q

histidine kinase

A

protein that senses extracellular signals and transfers phosphate to response regulator

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20
Q

signal transduction

A

based on phosphate transfer

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21
Q

response regulator

A

protein that receives phosphate from histidine kinase and activates output domain

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22
Q

binding of the signal

A

induces a conformation change inside the cell

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23
Q

what is caused by binding of signal?

A

the HATPase C domain cleaves ATP and place a phosphoric group on a histidine in the HisKA domain

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24
Q

phosphorelay

A

longer two-component system with histidine phosphotransfer protein (Hpt)

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25
Q

phosphorylation of receiver causes conformation change that activates

A

the output domain, the output domain then performs its function

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26
Q

most common output domain

A

helix-turn-helix dna binding domain, phosphorylation activates dna binding

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27
Q

diguanylate cyclases

A

output domain that synthesizes cyclic-di-GMP, a second messenger

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28
Q

initial signal

A

first messenger

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29
Q

small molecule signal affected by first messenger, transmit signals and modulate cellular responses

A

second messenger

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30
Q

second messengers exist as

A

intracellular pools

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31
Q

pseudomonas aeruginosa has

A

41 different c-di-GMP metabolizing proteins

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32
Q

almost all pools have

A

some sort of sensory domain (not just two component kind)

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33
Q

different kinds of sensory domains

A

Small molecules
Redox potential
Light
Voltage
Oxygen
Nutrients
Osmolarity
Antibiotics

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34
Q

second messengers can modulate

A

large cellular responses

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35
Q

many different proteins sense second messengers

A

respond in different ways

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36
Q

response ways after sensing second messengers

A

gene expression
post-transcriptional/post-translational regulation
allosteric enzyme control

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37
Q

in bacteria, c-di-GMP generally governs

A

surface attachment lifestyle

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38
Q

low c-di-GMP

A

motile

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39
Q

high c-di-GMP

A

sessile

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40
Q

the strident response- the ribosome has an associated protein

A

RelA

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41
Q

when an uncharged tRNA enters and leaves the A-site,

A

RelA catalyzes the production of (p)ppGpp

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42
Q

the more uncharged tRNA, the more (p)ppGpp

A
  • inhibits rRNA transcription
  • inhibits tRNA transcription
  • reduces mRNA transcription
  • increases proteolysis
    SLOWS CELL GROWTH
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43
Q

quorum sensing

A

population sensing mechanism in bacteria

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44
Q

quorum sensing- gram negative

A

acylated homoserine lactone autoinducers

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45
Q

autoinducer

A

small molecule used in quorum sensing to communicate between bacteria

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46
Q

quorum sensing- gram positive

A

small peptide autoinducers

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47
Q

what do bacteria do with quorum sensing?

A

pathogenesis and marine bioluminescent symbionts

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48
Q

pathogenesis

A

ability to cause diseases, some pathogens don’t express virulence factors until signficant population density

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49
Q

marine bioluminenscent symbionts

A
  • in fish and squid
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50
Q

hawaiian obtain squid- vibrio fischeri

A

quorum sensing timing mechanism so luminescent only at night
- counterilluminiation

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51
Q

catabolite repression

A

regulation of gene expression based on carbon/energy source availability

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52
Q

e. coli prefers glucose over

A

lactose

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53
Q

genes encoding enzymes that metabolize non-preferred carbon sources

A

may require transcriptional activation by CAP

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54
Q

CAP

A

protein that activates transcription of genes involved in metabolizing non-preferred carbon sources

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55
Q

transcriptional activation by CAP requires

A

binding by cyclic AMP (cAMP)

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56
Q

cAMP is made by

A

adenylate cyclase

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57
Q

a protein involved in glucose uptake

A

stimulates adenylate cyclase

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58
Q

cAMP with glucose

A

that protein is unavailable, no adenylate cyclase activity

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59
Q

cAMP without glucose

A

the protein is available, adenylate cyclase activity

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60
Q

cAMP

A

cyclic AMP, molecule that binds to CAP and activates transcription

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61
Q

adenylate cyclase

A

enzyme that synthesizes cAMP

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62
Q

diauxic growth

A

growth pattern with two distinct growth phases on different carbon sources

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63
Q

catabolite repression leads to

A

diauxic growth

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64
Q

d. growth chart (media with glucose and lactose)

A

lag, growth on glucose (catabolite repression) ON FIRST RISE, cAMP levels increase (catabolite enzymes induced) SECOND LAG, growth on lactose SECOND RISE, stationary

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65
Q

quorum sensing mechanism

A

by which bacteria communicate with each other

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66
Q

(p)ppGpp

A

molecule that inhibits various cellular processes and slows cell growth

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67
Q

firmicutes in the tree of life

A

second largest phylum in terms of cultured organisms (proteobacteria largest)

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68
Q

firmicutes originally grouped with

A

acintobacteria- both gram positive

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69
Q

firmicutes were separated based on GC content of chromosome

A

firmicutes- low GC
actinobacteria- high GC

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70
Q

16s rRNA sequencing show they are

A

different phyla, probably had a common ancestor

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71
Q

firmicutes all <50% GC content of

A

chromosome

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72
Q

most firmicutes have

A

no cell wall

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73
Q

firmicutes can subdivided based on

A

whether they make spores or not. FUNCTIONAL DEFINITION

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74
Q

bacillus is very common in

A

soils

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75
Q

bacillus is

A

aerobic or facultative anaerobes, often capable of using complex organic substrates (starch)

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76
Q

bacillus produce

A

extracellular lytic enzymes

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77
Q

some bacillus produce

A

antibiotics or other secondary metabolites

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78
Q

bacillus is genetically

A

facile (easy to use)
model for prokaryotic molecular/cell biology

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79
Q

bacillus subtitles endospore formation is

A

the third major model developmental system

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80
Q

how does bacillus decide when to sporulate?

A

through modulation of a complex phosphorelay

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81
Q

starvation induces

A

sporulation

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82
Q

kinA may respond to

A

ATP or redox levels

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83
Q

spo in sporulation (1)

A

spo0F transfers phosphate to Response Spo0B

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84
Q

spo in sporulation (2)

A

spo0B transfers phosphate to response regulator spo0A

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85
Q

spo0A turns on

A

sporulation

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86
Q

phosphates RapA and RapB dephosphorylate Spo0F,

A

preventing sporulation even though the signaling system is active

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87
Q

three other phosphates act on system,

A

Spo0F, Spo0B, Spo0A

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88
Q

same signals that induce sporulation also induce

A

competence (DNA uptake)

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89
Q

part of competence regulon is secretion of

A

pentapeptide outside cell

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90
Q

when pentapeptide builds up,

A

re-enters cell, shuts down phosphatases, sporulation starts

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91
Q

pseudo quorum

A

sensing system

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92
Q

sporulation is a time and energy

A

expensive process

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93
Q

sporulation is terminal

A

for the cell

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94
Q

sporulation is the last response to

A

starvation, worst case scenario

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95
Q

competence system inhibiting sporulation=

A

maybe there’s some DNA out there that can help

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96
Q

pseudo quorum sensing system allowing sporulation=

A

im not just in trouble, everyone around me is in trouble, time to bail

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97
Q

mother cell compartment

A

E then K

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98
Q

forespore compartment

A

F then G

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99
Q

parallel sigma cascades control

A

separate expression programs

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100
Q

initiation

A

H

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101
Q

B. anthracis causes

A

anthrax

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102
Q

cutaneous anthrax

A

large, black skin lesions

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103
Q

b. anthracis was the first bacterium

A

conclusively linked with a disease (ROBERT KOCH 1876)

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104
Q

b. cereus almost indistinguable from

A

b. anthracis

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105
Q

b. cereus can cause

A

food poisoning (fried rice syndrome)

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106
Q

b. cereus common soil organism

A

coating seeds with spores increases germination

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107
Q

b. thuringiensis

A

insect pathogen

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108
Q

b. thuringiensis genes for

A

Bt toxin cloned into plants (corn)

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109
Q

b. thuringiensis (bt toxin)

A

-insect pests eat cropland die, no effect on people
-transgenic crop hysteria

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110
Q

clostridium

A

obligate anaerobes- anoxic part of soil, intestinal microflora

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111
Q

some clostridium are capable fermenting amino acids/proteins

A

produce foul smells
putrefying meat/flesh

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112
Q

clostridium mostly known

A

for the famous pathogens

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113
Q

c. tetani causes tetanus

A

spores enter wound and germinate

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114
Q

tetanus toxin one of the strongest on earth

A
  • 175 nanograms cal kill 150 lb human
  • despite vaccine, 700k-1 million cases per year
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115
Q

toxin produced during

A

sporulation, released when mother cell lyses

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116
Q

toxins of c. tetani cause

A

motor neurons to continuously fire

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117
Q

risus sardonicus (c. tetani)

A

rigid smile

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118
Q

trismus (c. tetani)

A

lockjaw

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119
Q

opisthotonus (c. tetani)

A

rigid, arched back

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120
Q

c. difficile natural intestinal microflora in part of population

A

nosocomial

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121
Q

c. difficile can take over

A

intestine after it’s cleared of normal flora
- antibiotic

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122
Q

c. difficile causes pseudomembranous colitis

A
  • bloating, diarrhea, abdominal pain
  • can lead to toxic megacolon
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123
Q

c. perfringens natural intestinal microflora in part of population

A

nosocomial

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124
Q

c. perfringens can cause

A

some food poisoning, but that’s not the claim to fame

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125
Q

c. perfringens causes

A

gas gangrene

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126
Q

gas gangrene

A
  • infects wounds, big in war
  • necrotized muscle tissue, releases gas
  • causes corpses to swell up
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127
Q

c. botulinum first isolated in 1895

A

by emile van ermengem from home cured ham

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128
Q

botulinus- latin for sausage

A

apparently “sausage poisoning” was common in 18th century germany

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129
Q

botulism spores survive

A

canning/jarring

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130
Q

botulinum toxin causes flaccid muscle paralysis

A
  • muscles can’t contract
  • good: can treat cross-eyes, excessive blinking, excessive sweating, chronic migraine
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131
Q

questionable: botox

A

paralyzes expression muscles to prevent wrinkles

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132
Q

staphylococci commonly found on

A

skin and mucous membranes of some animals
- monkeys, birds, humans
- most ae harmless

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133
Q

staph. grow in the presence of

A

bile salts or 7.5% NaCl

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134
Q

high salt can be used as a selective agent

A

mannitol salt agar

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135
Q

staph. epidermidis is one of the most common

A

skin microflora (everyone has this, which is good)

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136
Q

staph. epi.

A
  • crowds out pathogens from skin niches
  • teichoic acids suppress inflammation response during wound repair
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137
Q

staph. epi. most common detected in lab culturing-

A

contamination

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138
Q

staph. epi. is practically non-pathogenic, except for…

A

biofilms on plastic devices
- catheters–blockage
- heart valves– endocarditis, sepsis

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139
Q

s. epi. biofilms very antibiotic resistant

A

generally have to replace the device

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140
Q

s. aureus

A
  • forms yellow colonies
  • 20% population are carriers
  • mostly known for MRSA
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141
Q

virulence factors staphyloxanthin

A

golden pigment, antioxidant, survives reactive oxygen species generated by immune system

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142
Q

virulence factors coagulase

A

surface enzyme causes blood-clotting, leads to fibrin coating cell, thought to aid in phagocytosis resistance

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143
Q

virulence factors capsule

A

extracellular polysaccharide that prevents phagocytosis, makes biofilm

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144
Q

s. aureus diseases (localized skin infection)

A
  • styes
  • boils
  • carbunkles- huge boils that leak pus
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145
Q

s. aureus diseases- diffuse skin infection

A

impetigo- large sores over skin surface
- break and leak pus or fluid to form scab
- most common among pre-school children or contact-sports athletes

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146
Q

s. aureus diseases non-cutaneous infections

A
  • septicemia
  • acute endocarditis
  • necrotizing pneumonia
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147
Q

septicemia

A

whole body inflammation
- septic arthritis

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148
Q

acute endocarditis

A

inflammation of heart valve

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149
Q

necrotizing pneumonia

A

lung infection causing death of the tissue

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150
Q

styes

A

infected glands around the eye

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151
Q

boils

A

infected, pus-filled hair follicle

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152
Q

carbunkles

A

huge boils that leak pus

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153
Q

toxinoses- reactions to S. aureus toxins

A
  • bacteriostatic antibiotics
  • scalded skin syndrome
  • toxic shock syndrome
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154
Q

scalded skin syndrome

A

fluid leakage through skin, causing inflammation, peeling, scaly, scabby skin

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155
Q

toxic shock syndrome

A

total body shock, can lead to coma, multiple organ failure, death

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156
Q

1978- proctor and gamble produces the rely long-lasting tampon

A

made of carboxymethylcellulose and compressed polyester beads
- absorbs 20x own weight
- also expands in width, so prevents leaks

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157
Q

1980- toxic shock syndrome defined, cases skyrocket

A

95% cases menstruating women using tampons

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158
Q

1982- tss linked to use of long-lasting tampons

A
  • synthetic materials and menstrual chemistry promote s. aureus growth
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159
Q

bacteremia

A

removal of tampons left in too long cause tears/wound

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160
Q

tampon materials themselves inert/non-toxic

A
  • only bacterial reaction to situation caused disease
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161
Q

tss led to legal definition of tampons as medical devices

A

more robust testing

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162
Q

s. saprophyticus

A
  • part of the normal vaginal microflora
  • causes 10-20% of urinary tract infections
  • particularly in sexually active young women
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163
Q

s. sap. can bind specifically to urothelium

A

surface tissue of urinary tract

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164
Q

spermicides and candid (fungal) infection

A

increase risk of disease
- perturb vaginal microflora

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165
Q

streptococcus

A

commensal- skin, mouth, intestine, upper respiratory tract

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166
Q

strep. divided into three groups based on reaction on blood agar

A

alpha-hemolytic
beta-hemolytic
gamma-hemolytic

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167
Q

alpha-hemolytic

A

h202 produced oxidizes iron in hemoglobin, turns green

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168
Q

beta-hemolytic

A

hemolysis lyses blood cells, clearing

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169
Q

gamma-hemolytic

A

does nothing to blood cells

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170
Q

(alpha) s. pneumoniae

A

aerotolerant anaerobe
leading cause of bacterial pneumonia
- also causes sinusitis, meningitis, otitis (ear infection)

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171
Q

(alpha) s. pneumoniae thought to cause disease through inflammation

A

inflammation illness- septicemia, septic arthritis, etc

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172
Q

(alpha) s. mutans- major contributor to dental cavities

A
  • ferment sugar to lactic acid
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173
Q

(alpha) s. mitis- insides of cheeks

A
  • may have survived in the surveyor 3 camera on the moon for 2 years
  • or someone sneezed on the camera after they brought it back
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174
Q

(alpha) s. salivarius

A

dorsal side of tongue

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175
Q

(beta) s. pyogenes

A

streptococcal pharyngitis
scarlet fever
rheumatic fever
necrotizing fascilitis

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176
Q

streptococcal pharyngitis

A

strep throat

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177
Q

scarlet fever

A
  • fever, sore throat, bright red tongue, rash
  • reaction to toxin produced by strains carrying t12 phage
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178
Q

rheumatic fever

A

inflammation involving heart, skin, joints, brain
- cross-reactivity of antibodies to streptococci with myocardium and joints

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179
Q

necrotizing fasciitis- “flesh-eating bacteria”

A

toxins cause destruction of muscle/skin

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180
Q

(beta) s. agalactiae

A

-pneumonia, meningitis in children/elderly
- colonize female reproductive tract
- can cause premature rupture of membrane during pregnancy
- transfer to infant

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181
Q

(gamma) enterococci

A

originally classified as strep. since they are very similar
- dna analysis indicated different genus

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182
Q

enterococci commensal in intestine

A
  • e. faecalis (90-95%), e. faecium (5-10%) clinical isolates
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183
Q

enterococci can cause disease

A

uti, endocarditis, meningitis
- emerging nosocomial infection
- naturally very antibiotic resistant, gaining more

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184
Q

due to high salt tolerance, enterococci has become standard for

A

fecal coliform testing at saltwater
- e. coli used for freshwater

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185
Q

staph and strep inhabit similar niches,

A

cause similar diseases

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186
Q

after culturing patient, staph and strep can be easily distinguished by growth pattern

A

growth pattern

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187
Q

staphylococcus

A

staph- greek for grape

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188
Q

streptococcus

A

strepto- greek for easily twisted, chain

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189
Q

staph divide sequentially along each axis

A

each division leaves a thick peptidoglycan rib

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190
Q

the peptidoglycan rib directs

A

which axis will be used next

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191
Q

lactic acid bacteria ferments sugars to lactic acid

A

make own acid-tolerate low pH

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192
Q

lactic acid bacteria generally require

A

many amino acids and vitamins

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193
Q

lactic acid bacteria divided phenotypically on other fermentation products

A
  • homofermentative
  • heterofermmentative
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194
Q

homofermentative

A

streptococci, lactococcus, lactobacillus, etc.
- only make lactic acid– emden-meyerhoff fermentation

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195
Q

heterofermmentative

A

leuconostoc, oenococcus, etc.
- make lactic acid, ethanol, and O2- pentose phosphate fermentation

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196
Q

sauerkraut, pickles

A

principally leuconostoc, mesenteries, others

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197
Q

kimchi

A

lactobacillus kimchii

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198
Q

salami

A

weissella, lactobacilli

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199
Q

beer (lambics)

A

yeast with 80 other bacteria, principally pediococcus

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200
Q

wine

A

yeast with other bacteria, oenococcus performs malolactic fermentation, creating rounder mouthfeel

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201
Q

listeria monocytogenes

A
  • 10% of human intestines, but also a lot in food products
  • most deadly food born pathogen (20-30% fatality in clinical cases)
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202
Q

listeriosis

A

septicemia, meningitis, encephalitis, pneumonia, and spontaneous abortion/stillbirth in pregnant women

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203
Q

(listeriosis) women advised to

A

avoid soft cheeses during pregnancy, good reason for everyone to avoid raw milk products

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204
Q

(listeria) moderately psychophilic- can grow in refrigerated meats

A

fda has approved cocktail of six bacteriophages as food additives

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205
Q

live, attenuated L. monocytogenes being developed as

A

cervical cancer vaccine

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206
Q

l. monocytogenes flagella inactive at 37ºC,

A

move in eukaryotic cells by polymerizing actin behind them, pushed like rocket

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207
Q

mollicutes- “soft/pilable skin”

A
  • lack cell wall
  • animal pathogens
  • plant pathogens
  • parasitic lifestyle
  • basis for the first artificial life forms
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208
Q

mollicutes- animal pathogens

A

mycoplasma, ureaplasma
- lungs, urinary tract

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209
Q

mollicutes- plant pathogens

A

phytoplasma, spiroplasma

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210
Q

mollicutes- parasitic lifestyle- degraded genome

A
  • require host for many biological molecules
  • m. genitalium genome 580 kbp, 482 genes
  • smallest known Buchner aphidicola, 357 genes
  • some candidate organisms estimated between 169- 242 genes
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211
Q

mycoplasma, minimal genome project started with M. genitalium genome (482 genes)

A

and deleted genes until they found the fewest that could support life (382 genes)

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212
Q

mycoplasma, minimal genome project: 2008

A

synthetically synthesized genome with 382 genes and included watermarks

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213
Q

watermarks

A

small sequences that make peptides coded peptides

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214
Q

mycoplasma as artificial life

A

-synthetically made the M. mycoses 1.2m genome from computer file
- put into m. capricolum cell with original dna removed
- new cell was viable and behaved like M. mycoses (synthia)

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215
Q

july 2012- made computer simulation of m. genitalium

A

doubles in computer every 10 hrs, like in real life
- can now do experiments in M. genital without having to work with organism

216
Q

protein export

A

moving a protein across a membrane

217
Q

protein secretion

A

moving a protein into the extracellular medium

218
Q

bacteria have multiple destinations proteins can go- gram positive

A

Cytoplasm
Membrane
Cell wall
Medium

219
Q

bacteria have multiple destinations proteins can go- gram neg

A

Cytoplasm
Inner Membrane
Periplasm
Cell Wall (rare)
Outer membrane
Medium

220
Q

getting proteins across the membrane- general protein export

A
  • the sec system (or general secretory pathway)
  • major protein export system in all bacteria
221
Q

general protein export functions to

A

-translocate proteins across the cytoplasmic membrane
-embed integral membrane proteins into the cytoplasmic membrane

222
Q

protein export is determined by a signal (leader) sequence

A

-found at n-terminus of protein
- NOT A SPECIFIC PROTEIN SEQUENCE

223
Q

three general regions of signal sequence

A
  • a basic region (1-3 positive amino acids)
  • hydrophobic regions (about 15 aminos acids, inserts into membrane)
  • signal peptidase recognition region (site where signal peptide is cut, removed from rest of protein if necessary)
224
Q

signal peptidase cleave site

A

site where signal peptide is cut, removed from rest of protein if necessary

225
Q

protein + signal=

A

preprotein

226
Q

secB (chaperone) binds newly translated protein,

A

prevent secondary/tertiary structure protein folding would interfere with export

227
Q

secB hands protein off to SecA,

A

protein associated with SecY/SecE transmembrane pore

228
Q

basic region of signal sequence associated with phosphate head group

A

of phospholipid

229
Q

hydrophobic region of signal peptide begins

A

inserting into membrane core

230
Q

carboxy terminus of signal sequence flips to

A

periplasmic side

231
Q

pre protein enters the

A

translocate channel

232
Q

secA disassociates

A

requires atp, small amount of protein translocated

233
Q

proton motive force

A

drives rest of protein translocation

234
Q

signal peptidase cleaves

A

protein off membrane (optional)

235
Q

integral membrane proteins, exported proteins can have

A

stop transfer signals
- protein sequences that stop transfer, enter membrane

236
Q

integral membrane proteins can also have

A

secondary export sequences
- reinitiate export at a second site

237
Q

integral membrane proteins- combination of these signals lead to

A

membrane proteins of varying topologies

238
Q

targeting of many integral inner membrane proteins is performed by the signal recognition particle

A
  • SRP recognizes signal peptide as ribosome translates
  • Pauses translation and brings signal peptide to Sec system
239
Q

second export method- TAT Export (twin arginine translocation)

A

found throughout all bacteria, archaea, plant chloroplasts and mitochondria

240
Q

TAT Export translocates folded proteins across cytoplasmic membrane

A
  • Extracellular/periplasmic space harsher environment for folding
  • Some proteins may required cytoplasmic chaperones for proper folding
  • May require cofactors found in cytoplasm
  • Translocates multiprotein complexes, including those without export signals (hitchhikers)
241
Q

TAT signal peptide-sec

A

both have general features, but TAT has specific sequence

242
Q

TAT signal peptide- n-region

A

positively charged

243
Q

TAT signal peptide- h-region

A

hydrophobic

244
Q

TAT signal peptide- C-region

A

signal peptide recognition

245
Q

what about the other destinations? periplasmic proteins

A

already in periplasm, no direction necessary

246
Q

what about the other destinations? cell wall proteins

A
  • In appropriate compartment after export
  • Covalently attached to peptidoglycan by sortases
  • Recognize C-terminal sortase sequence
247
Q

what about the other destinations? outer membrane proteins

A
  • No specialized membrane-embedding system
  • Self assemble into outer membrane
248
Q

what about the other destinations? outside the cell- secretion systems

A

a gram negative problem

249
Q

type 2 secretion

A
  • major secretion pathway
  • related to type iv pilus assembly
  • requires proteins to be transported to periplasm by sec/tat pathway first
  • secretion signal not well-understood
  • large multiprotein complex
250
Q

type 2 secretion- large multiprotein complex

A
  • inner membrane/cytoplasmic platform powered by ATP
  • pseudopilus used as piston to push folded proteins through outer membrane pore
251
Q

type 1 secretion

A
  • one family of efflux pumps
252
Q

efflux pumps

A

protein-based transporters
– Toxins
–Antibiotics
–Heavy metals

253
Q

all families of efflux pumps have

A

same basic organization

254
Q

type 1 secretion uses atp to

A

translocate proteins

255
Q

type 1 secretion recognizes c-terminal

A

motif on exported protein (not cleaved)

256
Q

type 1 secretion often has 1

A

transporter for 1 protein

257
Q

type 3 secretion

A

-used for pathogenesis
-related to flagellum structure

258
Q

type 3 secretion- related to flagellum structure

A
  • Share basal body structure
  • Flagellum has built in protein secretion mechanism to form structure
259
Q

type 3 secretion proteins secreted:

A
  • Probably uses ATP
  • Recognized by N-terminal signal (not cleaved)
260
Q

needle

A

tube that connects bacterial cell to eukaryotic target cell

261
Q

type IV secretion used for

A
  • pathogenesis
  • translocation of oncogenic DNA/effectors
  • bacterial conjugation
  • competence
262
Q

type IV secretion structure

A

pilus structure with macromolecules passing through pilus tube

263
Q

type IV secretion proteins secreted

A
  • c-terminal secretion signal and accessory factors/chaperones
  • likely powered by ATP
  • cytoplasm to outside, some examples of periplasm to outside
264
Q

type V secretion

A
  • autotransporters or two-partner secretion
  • secreted to periplasm by Sec/Tat
265
Q

type V secretion- autotransporter

A
  • C-terminal region of protein forms beta-barrel in outer membrane
  • N-terminal portion passes through barrel
  • Either stay as is, or be released from barrel by proteolysis (autoproteolysis or dedicated protease)
266
Q

type V secretion- two partner secretion

A

same as auto transporters except beta barrel is separate protein

267
Q

type VI secretion

A
  • found in about 1/4 of sequenced gram negative genomes
  • similar to tail/spike of T4 phage
  • symbiosis, pathogenesis, intermicrobial interaction/competition
268
Q

flagellar motility is based on

A

rotation of the flagellum filaments

269
Q

the helical structure of flagellum filaments/ bundles provides

A

propulsion

270
Q

e. coli has peritrichous flagella that form a helical

A

bundle when swimming smoothly (running)

271
Q

when e coli wants to change direction,

A

it changes the rotation of its flagella

272
Q

this rotational change causes the flagella to fly apart from the bundle and

A

rotate separately, reorienting the cell (TUMBLE)

273
Q

changing the rotation of the flagellum to alter the running/ tumbling behavior is

A

a generally conserved aspect of swimming motility regardless of the number and placement of the flagella

274
Q

tumbling frequency

A

general pattern of running and tumbling

275
Q

tumbling frequency can be altered

A

in response to a chemical stimulus

276
Q

chemotaxis

A
  • chemoattractant
  • chemorepellent
277
Q

chemoattractant

A

increases running, decreases tumbling

278
Q

chemorepellent

A

decreases running, increases tumbling

279
Q

alteration of tumbling frequency can lead to

A

net translocation of cells up or down chemical gradients

280
Q

swimming cells

A

random walkc

281
Q

hemotaxis creates a

A

biased walk

282
Q

running/tumbling behavior is controlled by the

A

chemotaxis signaling system (many similarities to two-component signaling systems)

283
Q

CheA

A

similar to histidine kinase

284
Q

CheW

A

adaptor protein

285
Q

MCP

A

methyl-accepting chemotaxis protein

286
Q

CheY- similar to response regulator

A

induces tumbling (CW or CCW depends on organism)

287
Q

balance of CheY and CheY-P

A

determines tumbling frequency

288
Q

binding of chemoattractant to MCP shuts off phosphorylation pathway

A

decreases CheY-P, reduces tumbling

289
Q

chemorepellents induce

A

more phosphorylation

290
Q

bacteria sense chemoeffectors over time

A

the adaptation response

291
Q

CheB

A

removes methyl groups from MCPs when phosphorylated

292
Q

CheR

A

puts methyl groups on MCPs constitutively

293
Q

CheR- methyl groups

A

inactivate MCPs

294
Q

explains why cells respond to chemical gradients

A

Require increasing concentrations of chemicals to overcome adaptation

294
Q

adaptation response necessary so

A

don’t shoot past areas with desired chemicals

295
Q

Cells sensing/sampling chemical concentration over time, not in space

A
  • Important because cells too small to sense chemical gradients over body length
  • Balance of stimulus and adaptation way of comparing chemical concentration between time points
  • Chemical Marco Polo
296
Q

the problem of “gain”- chemotaxis can respond to a chemical

A

at concentrations over 5 orders of magnitude

297
Q

the problem of “gain”- chemotaxis response

A
  • Same behavior response to 50 molecules as to 5,000,000
  • MCP’s only have one substrate binding affinity
  • Substrate way below affinity, virtually none bound, should get no response induction
298
Q

chemotaxis systems must have a way to generate “gain”

A
  • Amplify low level signals to create as robust a response as a larger signal
  • Pumping up the Volume
299
Q

a possible solution to “gain”

A

binding of chemoeffector to one MCP may affect conformation or those around it such that their signaling state is changed even though they are not bound to a chemoaffector

300
Q

MCPs are found in dimers

A

dimers binders to groups of three
- trimers of dimers hexagonally pack into chemoreceptor arrays

301
Q

phototaxis

A

lighta

302
Q

aerotaxis

A

oxygen- can be o2 directly or redox state of cytochrome pool

303
Q

magnetotaxis

A
  • Some bacteria produce magnetosomes, chains of magnetite crystals in cell
  • Cells align along magnetic pole of the Earth
  • Northern Hemisphere cells swim to the North Pole, opposite in Southern Hemisphere
  • Poles underground, causes cells to move up/down water column
  • Magnetotactic bacteria obligate microaerophiles/anaerobes
304
Q

surface motility using flagella- swarming motility

A

-requires peritrichous flagella
- cells gather together and move as groups
- requires production of a surfactant

305
Q

surface motility using flagella- swarming motility requires p. flagella

A
  • Cells will often swim with one flagellum, but change to multiple flagella to swarm
  • Swarming flagella genetically distinct from swimming flagella, e.g. Vibrio parahaemolyticus
306
Q

cells gather and move as groups

A

“rafts”- swarming cells fall out of rafts and become non-motile

307
Q

surface motility using flagella- swarming motility require production of surfactant

A

chemical that reduces surface tension, essentially a lubricant

308
Q

twitching motility

A

Uses polar Type IV pili
Pilus extends and attaches to substrate
Pilus retracts, pulling cell forward

309
Q

Gliding Motility

A
  • work of myxococcus xanthus
  • attachment of focal adhesion sites to a substrate
  • adhesion sites cycle around the cell proppeling it forward
310
Q

M. xapnthus secretes a polyscarrachride slime

A
  • Likely serves as self-made adhesion substrate
  • Analogous to laying down track in front of a moving train
311
Q

Mycoplasma are obligate

A

pathogens/parasites

312
Q

M. pneumoniae

A

walking pneumonia

313
Q

Mycoplasma are smallest genomes of all bacteria

A
  • 580-860 kbps (~1/10 of most bacteria)
  • Likely genome degraded
  • Relies on host for many essential functions
    —-Cannot make purines
314
Q

mycoplasma lack a cell wall

A

so they have unusual cell shape

315
Q

mycoplasma UGA codon not to stop,

A

tyyptophan

316
Q

mycoplasma move by

A

proteins on their terminal organelle

317
Q

actinobacteria- gram

A

positive

318
Q

actinobacteria- shape

A

rods or filamentous

319
Q

actinobacteria- respiration

A

most respire aerobically, some fermentation

320
Q

actinobacteria- location

A

common in soils, some pathogens

321
Q

actinobacteria- diversity

A

large diversity at suborder level

322
Q

actinobacteria- >50%

A

GC content genome

323
Q

Deinococcus radiodurans

A

Bacteria – carries 4-10 copies of its chromosome
- Can survive 15,000 Grays ionizing radiation with 37% loss of viability
- 5 Grays will kill a human

324
Q

deinococcus is NOT in

A

the actinobacteria

325
Q

kineococcus and rubrobacter ARE

A

in the actinobacteria

326
Q

kineococcus and rubrobacter are as good at radiation resistance as

A

deinococcus

327
Q

propionic acid bacteria

A
  • aerotolerant anaerobes
  • can ferment lactic acid
  • unique ability to propionic acid and co2 from fermentation
327
Q

propionic acid bacteria- fermentation

A

unusual transcacrboxylase enzymes acting on succinate

328
Q

propionic acid bacteria- can ferment lactic acid

A

fermentation of a fermentation product is “secondary fermentation”

329
Q

propionibacterium acnes

A

lives on skin, sweat glands, sebaceous glands–> causes acne

330
Q

propionibacterium freudenreichii

A
  • used for swiss cheese, propionic acid flavor, co2 for holes
  • same type of organism that causes pimples makes swiss cheese
331
Q

bifidobacteria-anaerobes

A
  • one of the most common commensal bacteria
    —- one of the most common probiotic organisms
332
Q

bifidobacteria dominate infant gut microflora

A
  • infant associated bifidobacteria display milk oligasaccharide utilization
  • adult-associated bifidobacteria display plant oligosaccharide utilization
333
Q

corynebacteria are

A
  • facultative anaerobes
  • common in soil, human commensal
  • rods, often club shaped
334
Q

corynebacterium diptheriae

A
  • causes diphtheria
  • cells infected with lysogenic B phage– carries toxin gene
  • colonize lesion in upper respiratory tract
  • general antibiotic sensitive, easily controlled by vaccination
335
Q

corynebacterium diptheriae- lysogenic B phage

A
  • toxin gene depressed by low iron
336
Q

corynebacterium diptheriae- lesion

A
  • toxin causes necrotic injury to epithelial cells
  • platelets leak out, form pseudomembrane of dead cells, fibrin
  • c. diphtheria grows in it
  • can spread to lungs- suffocation, also toxin illnesses
337
Q

corynebacterium diptheriae- general antibiotic sensitive

A
  • 3 cases in US between 2000-2007
  • fall of USSR- vaccination decreased, 200k, 5k deaths in 1998
338
Q

mycobacterium tuberculosis id

A

1-10 cells

339
Q

mycobacterium tuberculosis- first line treatment

A

rifampicin and isoniazid

340
Q

mycobacterium tuberculosis (multi-drug resistant)

A

resistant to first line

341
Q

mycobacterium tuberculosis- extensively drug resistant (XDR)

A

resistant to first and second line

342
Q

mycobacteria

A
  • Aerobic, mostly aquatic
  • Can live in chlorinated tap water
  • Some obligate pathogens
343
Q

Mycobacteria tuberculosis

A
  • Causes Tuberculosis (Consumption)
  • Infects alveolar macrophages
  • 50% mortality if untreated
  • One-third of population is infected (nearly 3 billion)
    ——80% Asia, 5-10% US
344
Q

Mycobacteria leprae

A
  • Causes Hansen’s Disease (Leprosy)
  • Divides every 15-20 days
    —-Never successfully cultured outside of cells
  • Transmitted by close, prolonged contact – nasal droplets
    ——Major source for US is from armadillos (including Mississippi)
345
Q

Mycobacteria leprae 2

A
  • Entry and exit route from humans not known (disease not understood)
  • Primarily infects nerve cells – inflammation response kills nerves
    —–Numbness –> untended lesions –> necrosis and limb removal
346
Q

mycelia are acid fast

A

mycobacteria appear weakly gram positive or variable
- acid fast due to their unusual cell wall

347
Q

acid fast staining procedure

A
  • Initial stain taken by cells
  • Decolorize with acid/alcohol mixture
  • Counterstain
  • Acid Fast bacteria retain initial stain
348
Q

myolic acids of m. tuberculosis

A
  • creates outer layer 3-4 times thick as normal membrane
349
Q

actinomyces

A
  • facultive anaerobes, but prefer anaerobic
  • similar to nocardia in lifestyle
  • grow as branching filaments, fungi-like
350
Q

actinomyces location and characteristics

A
  • very common in soil, normal commensal of gingival area of mouth
  • opportunistic pathogen in mouth
  • dental procedures
  • actinomyces Israelii most common pathogen
351
Q

actinomycetes- streptomyces coelicolor

A
  • model developmental organism
  • closest thing to a bacterial fungus
  • grows in hyphae
  • well-known and utilized for secondary metabolite production
352
Q

streptomyces coelicolor- hyphae

A
  • long, branching filaments
  • grow below surface (soil, agar)
  • produces aerial hyphae, spores develop at the tip
353
Q

streptomyces coelicolor- secondary metabolite production

A
  • Antibiotics, antifungals, antiparasitics, geosmin, etc
  • Two-thirds of clinical antibiotics of natural origin from Actinomycetes
354
Q

coriobacterium

A
  • Anaerobe
  • Ferments glucose to acetic acid, lactic acid, ethanol, CO2, H2
  • Commensal symbiont in the midgut of Firebugs
355
Q

gut microflora

A
  • huge field of research
  • the types of microbes that live in insect guts determine what they can eat
356
Q

gut microflora- lower termites

A
  • Termites ingest wood pulp (cellulose, lignin), can’t metabolize it
  • Some bacteria ferment to short chain fatty acids
  • Protists metabolize to CO2 + H2
  • wood pulp nitrogen poor
    -hindgut
357
Q

gut microflora- protists metabolization

A
  • Bacterial exo/endosymbionts with protists
    —–Methanogenesis (CO2 + H2  CH4)
    ——Acetogenesis (CO2 + H2  Acetate)
358
Q

gut microflora- wood pulp nitrogen poor

A
  • bacteria recycle uric acid
  • nitrogen fixation
359
Q

hindgut

A

anaerobic digestor– up to 1/3 body weight of termite

360
Q

ant agriculture

A
  • ants collect plant material, return to special garden in nest
  • pulp material, inoculate with fungus
  • ants carry actinobacteria on cuticle
361
Q

ant agriculture- pulp material

A
  • Single cultivar of fungus, cannot live outside nest
  • Fungus grows, produces gongylidia
    —– Swollen hyphal tips rich in lipids/carbohydrates
    —– Ants harvest gongylidia for food
362
Q

ant agriculture- escovopsis

A

specifically infects fungal gardens

363
Q

ant agriculture- carry actinobacteria (streptomyces, pseudonocardia)

A
  • Bacteria produce antibiotics/antifungals
  • Ants use bacteria to “weed” their garden
364
Q

cyanobacteria

A

oxygenic photosynthesis

365
Q

chloroflexi

A

an oxygenic photosynthesis, green non-sulfur

366
Q

chlorobi

A

anoxygenic photosynthesis, green sulfur

367
Q

cyanobacteria

A
  • gram negative
  • oxygenic photosynthesis, calvin cycle carbon fixation
  • widespread in water (fresh/salt)
  • “blue-green algae”
368
Q

cyanobacteria- photosynthesis, carbon fixation

A

Chlorophyll a and phycobilins (secondary pigments) in thylakoid membranes

369
Q

cyanobacteria- in water

A

surface soil layer, even in deserts

370
Q

cyanobacteria- “blue-green algae”

A
  • Phycobilins give blue color
  • Weren’t considered bacteria
  • 16S rRNA sequencing clearly shows prokaryote
371
Q

nitrogen starvation induces

A

heterocyst formation

372
Q

heterocysts

A

terminally differentiated cells

373
Q

heterocysts- 3 exterior layers

A
  • Glycolipid
  • Compacted polysaccharide
  • Un-compacted polysaccharide
374
Q

heterocysts-

A

degration of photosystem 2
— ceases oxygenic photosynthesis
scavenging of excess o2
— production of nitrogenase

cell dedicated to n2 fixation

375
Q

heterocyst cannot fix carbon

A

need from other cells

376
Q

regular cells need nitrogen

A

from heterocyst

377
Q

metabolites diffuse

A

through the filament

378
Q

heterocyst form at regular intervals in filament

A

Cells starve for nitrogen
Cell turning into heterocyst produces small peptide that inhibits heterocyst formation in adjacent cells
Peptide forms gradient through filament
Where peptide concentration low enough, heterocyst develops

379
Q

why have regular spaced heterocyst?

A
  • Terminally differentiated and energetically costly
  • Spaced to have maximum effect with minimum number
380
Q

heterocyst- akinetes

A

Large granular-looking cells
Induced by starvation
Granules of storage polymers
Glycogen – carbon
Cyanophycin – nitrogen
Metabolically dormant
Cold and desiccation resistant
Not heat resistant
Not a spore, more of a cyst

381
Q

akinetes often form in patterns when heterocysts are present

A
  • pattern dependent on organism
  • random when no heterocyst present
382
Q

some genes in cyanobacteria display patterns of gene expression based on

A

diurnal (light/dark cycle)

383
Q

synechocystis

A

Hooked a bioluminescent reporter up to a gene encoding part of Photosystem II

Measured luminescence over time

384
Q

64% of all synechocystis genes display “circadian rhythms”

A

Cyanobacteria circadian rhythm controlled by “molecular clock”
– KaiA, KaiB, KaiC proteins
– KaiC phosphorylated on multiple sites
– Phosphorylation level changes over time

385
Q

circadian rhythm

A

repeated biological process based on 24 hour light/dark cycle
- Cycle sensitive to light (resetting)
- Found in bacteria, fungi, plants, animals (humans)

386
Q

molecular clock can be reconstituted in vitro

A

KaiA + KaiB + KaiC + ATP

387
Q

circadian rhythms provide selectable advantage to cyanobacteria

A

89% of photosynthesis genes circadian regulated

388
Q

Biotechnology with cyanobacteria during day

A

Photosynthesis, fix carbon, produce ethanol
Ethanol evaporates into headspace of reaction chamber

389
Q

Biotechnology with cyanobacteria- during night

A

Ethanol condenses on sides of chamber (solar trap/still)
Collected and purified

390
Q

Biotechnology with cyanobacteria- sept 2012

A

Algenol claims make 7,000 gallons/acre/day
Meet US gas needs by 2025
Require area 1/10 of other bioethanol processes (corn)
Half a county worth of land
Requires only freshwater, minerals

391
Q

prochlorophytes

A

Subgroup within cyanobacteria
Use Chlorophyll b instead of phycobilins
Can be very small cells
Can be in open ocean
Prochlorococcus
Can be marine invertabrate symbiont
Prochloron (sea squirt)
Nearest common ancestor to chloroplasts

392
Q

chloroflexi

A
  • Green non-sulfur bacteria
  • Anoxygenic photosynthesis
  • Use organic carbon sources
  • Gram Positive cell wall (stain Gram Negative)
  • Mostly thermophiles (hot springs)
393
Q

chloroflexi- photosynthesis

A

Do not use H2S as electron donor
—-Some do

394
Q

chloroflexi- gram + cell wall

A

Different peptidoglycan size/composition
No peptidoglycan, use S-layer

395
Q

chloroflexi- thermophiles

A

Some mesophilic chemoheterotrophs found

396
Q

Herpetosiphon aurantiacus

A
  • Aerobic heterotroph common in high nutrient environments
  • Long filaments, able to glide and prey on other bacteria
397
Q

Herpetosiphon giganteus

A

16 restriction enzyme

398
Q

Herpetosiphon giganteus – 16 restriction enzyme systems
Dehalococcoides ethenogenes

A

can metabolize chlorinated industrial solvents
Recent analysis suggests might be distinct lineage from Chloroflexi

399
Q

chlorobi

A
  • green sulfur bacteria
  • Anoxygenic photosynthesis
  • Fix carbon by reverse TCA, not Calvin Cycle
  • contain Chlorosomes
400
Q

chlorobi- photosynthesis

A
  • use H2S as electron donor
  • Elemental S waste deposited outside cell
  • Not in periplasm, like purple photosynthetic bacteria
401
Q

chlorobi- chromosomes

A

Efficient light harvesting complexes, use low intensity
Live deeper in water column where H2S concentration higher
—-Can live at 100 m depth, few photons/chlorophyll/day
One found living near “black smoker” 2,500 meters ocean depth
—-Living off glow of vent, no sunlight gets down that far

402
Q

chlorosomes

A

Contain huge stacks of pigment – no protein

403
Q

deinococcus- thermus clade

A

Gram Negative, stain Gram Positive due to thick peptidoglycan layer
Resistant to hazardous environments

404
Q

Deinococcus radiodurans

A

Bacteria – carries 4-10 copies of its chromosome
Can survive 15,000 Grays ionizing radiation with 37% loss of viability
5 Grays will kill a human

405
Q

Thermus- Thermus aquaticus

A
  • identified from hot spring in yellowstone
  • growth range- 50º to 80ºC
  • chemolithoautotroph
  • source of taq polymerase
406
Q

Thermus- Thermus aquaticus- Taq polymerase

A
  • Thermostable DNA polymerase
  • Sparked development of PCR
    —-Could be heated repeatedly without losing activity
  • No 3’ exonuclease
    — More error prone, 1 in 1000 bases
  • Puts A’s on the ends of PCR fragments
407
Q

bacterioides

A

one of two phyla that dominate gut microflora (firmicutes)
—- 10^10-10^11 cells/gram human feces
- digests soluble dietary fiber
—- 18% genome dedicated to polysaccharide utilization

408
Q

bacteroides health risks

A

Usually harmless, but can act as repository of antibiotic resistance systems that spread to pathogens
B. thetaiotaomicron, B. fragilis
Opportunistic pathogens, common abdominal infection

409
Q

bacteroides fun fact

A

Bacteroides in guts of native Japanese have special enzyme for degrading seaweed sulfonated-polysaccharides (not found in Westerners)
—Picked it up from marine bacterium Zobellia galactanivorans by horizontal gene transfer

410
Q

spirochetes

A
  • Long, thin, tightly-spiraled cells
  • Heterotrophs
  • Have flagella in the periplasm (axial filaments)
  • Widespread in water
  • Several important pathogens
411
Q

leptospira

A
  • causes leptospirosis (canefield fever, fort bragg fever, black jaundice, rat chasers yellows)
  • infects most mammals
    — causes disease in dogs
    — transmitted to humans through contact with animal urine
  • common among ribal native americans
    — constant contact with infected waters
  • outbreaks in ww1
    — pooled water in trenches (gallipoli)
    2010- killed british rower andy holmes
412
Q

leptospira symptoms

A

Phase 1 – flu-like (fever, chills, ache, vomiting), then clears up
Phase 2 – meningitis, renal failure, liver failure (jaundice)

413
Q

Borrelia burgdorferi

A

Causes Lyme Disease (endemic to North America)
Identified in Lyme, Connecticut
- does not require Fe, uses Mn for all processed
—- works well in pathogenesis

414
Q

Borrelia burgdorferi
transmission

A

Transmitted by Ixodes ticks
– Lives in digestive tract tick
– Transmitted when bacterium travels to salivary gland while tick is feeding
– Usually only occurs 24 after feeding initiated

415
Q

lyme disease- early localized infection

A

Bullseye rash at bite, potentially flu-like symptoms, ~20% asymptomatic

416
Q

lyme disease- early disseminated infection

A

bacteria, rashes at other sites, potentially facial palsy/meningitis

417
Q

lyme disease- Late disseminated infection

A

shooting pains, numbness, severe joint pain, paraplegia

Psychosis – anxiety, panic attacks, delusions, depersonalization (detachment from reality)

418
Q

Treponema pallidum
causes and transmitted through

A
  • Causes Syphilis
  • Transmitted through sexual contact
    —– Also mother-to-fetus during pregnancy/birth (congenital syphilis)
419
Q

Treponema pallidum
stages

A

Stage 1 (3-90 days) – single chancre (firm, painless, non-itchy ulceration) point of infection
Stage 2 (4-10 weeks) – rash (red papules, white pustules, both infectious) over torso/extremities, characteristically on palms and soles
Stage 3 (10 weeks to 3 years) – asymptomatic latency
Stage 4 (3-15 years) – cardiovascular, neurological, gummatous (gummas = soft, tumor-like balls of inflammation on skin/bone/liver)

420
Q

Treponema pallidum
- congenital

A

Congenital – two-thirds born asymptomatic, develop later
Rash, fever, neurosyphilis, large liver/spleen  deformed clavicle, “saber shin”, “saddle nose”

421
Q

Syphilis in History

A

The Columbian Exchange – exchange plants, animals, people and diseases between Europe and Americas
Evidence indicates Syphilis in Americas, brought back to Europe
First European outbreak recorded in 1495 – French troops besieging Naples, Italy (Spanish mercenaries from Columbus’ trip)
Native Americans gave Europeans syphilis, Europeans gave Native Americans smallpox
Major cause of death during the Renaissance
Much more virulent then than now

422
Q

syphillis name coined by fracastoro

A

Made Syphilis name of sheepherder in poem that first contracted disease, then used in own medical textbook

423
Q

tuskegee syphilis study

A

USPHS never told them they had syphilis and didnt get treatment
— 28 died of syphilis, 100 of related complications, 40 wives contracted disease, 19 children congenital syphilis

424
Q

T. pallidum subspecies cause other diseases
- beiel

A

arid countries of Mediterranean, West Africa
– Small mucosal patch in mouth, eroding lesions on body, inflammation of leg bones, gummas on nose/mouth
– Transmitted by mouth/mouth contact, sharing utensils

425
Q

T. pallidum subspecies cause other diseases
- pinta

A

Mexico, Central/South America
Papule at contact, flat lesions over body, mixture of hyperpigmentation/depigmentation
Transmitted by skin/skin contact

426
Q

T. pallidum subspecies cause other diseases
- yaws

A

humid tropical latitudes
Warty nodules, widespread skin ulcers, destruction of joints/soft tissue
Transmitted by skin/lesion contact
Been with homonids 1.5 million years

427
Q

chlamydia

A

Obligate intracellular pathogens
Humans, mammals, birds, protozoa
Little biosynthetic capability (~600 genes)
Have an unusual cell cycle, two forms
Elementary body – similar to spore
Infectious form, taken into cell by phagocytosis
Turns into reticulate body
Reticulate body – growth form
Grows by binary fission
New cells turn into Elementary bodies
Host cell bursts, releasing Elementary bodies

428
Q

Chlamydia trachomatis

A

Causes Chlamydia
Most common STD
2.5 million cases/year in US
- eye infection
—- Was a major cause of blindness until ~15 years ago (now 3.6%)

429
Q

Chlamydia trachomatis
- presentation

A

Men – clear/white discharge from penis

Women – “Silent Epidemic”, 50-70% cases asymptomatic
Pelvic Inflammatory Disease (inflammation of reproductive organs)
Scarring, ectopic pregnancy, spontaneous abortion, sterility
Passed to child during birth

430
Q

Verrucomicrobia

A

New recognized phylum
Few cultured species
Environment DNA analysis suggests may be one of the most abundant bacteria in water/soil
Verrucamicrobium spinosum was first described
Has small stalks, make cell look “warty”

431
Q

Epixenosomes

A

Euplotidium is marine unicellular ciliate
Has on surface a zones of epibionts
Bacteria that live on the outside of another organism
Bacteria belong to Verrucomicrobia
Bacteria attach and grow for a while by binary fission
Then differentiate into epixenosomes
Cell have coiled protein filament, surrounded by “basket” of tubulin

432
Q

When Euplotidium is attacked by another ciliate, Litonotus lamella, the “bacteria” sense it

A

Can be stimulated in lab by adrenaline
Bacteria respond in activation of cyclic-AMP system

433
Q

Bacteria burst, extend 40mm long filament, tipped with compacted DNA

A

Fights off predator (unknown mechanism)
Similar in concept to jellyfish nematocyst

434
Q

Fusobacteria

A

Anaerobic, Gram Negative
Rods with tapered ends
Ferment carbohydrates/amino acids
Butyrate, acetic acid products
Commonly found in mouth, other mucus membranes
Cells exceptionally good at sticking to other cells
Colonize established biofilms in mouth (plaque)
Cause disease

435
Q

Disease causing Fusobacteria
Streptobacillus moniliformis

A

Causes Haverhill Fever (form of Rat-Bite Fever)
Spirochaete-based Rat-Bite Fever – in Japan called Sodoku
Bite or exposure to mucosal secretions/urine from rodents
Flu-like symptoms, rash
Generally not fatal, especially with treatment

436
Q

Disease causing Fusobacteria
-Fusobacterium polymorphum

A

Found in human gingival crevice
Implicated in various periodontal diseases

437
Q

Disease causing Fusobacteria
- Fusobacterium necrophorum

A

10% acute sore throats, 21% recurring sore throats, 23% peritonsillar abscesses
Lemierre’s Syndrome
Bacteremia leading to thrombosis (blockage) of jugular vein, then to lungs, brain vessels
Often F. necrophorum secondary infection on primary throat infection (Strep)

438
Q

Caldiserica
Caldisericum exile

A

Gram Negative, anaerobic thermophile
65oC optimum
10.4 hr doubling time
Non-sulfate sulfur reducer
Multicellular filaments
Single polar flagellum, for some reason

439
Q

Gemmatimonadetes
Gemmatimonas aurantiaca

A

Gram Negative, facultative anaerobe
Heterotrophic
Common in soil
Produces unusual carotenoids
Grows slowly
2 weeks for colony to arise

440
Q

Elusimicrobia
Elusimicrobium minitum

A

Only member of Termite Group 1 phylum
Isolated from scarab beetle intestine
Gram Negative anaerobe
Ferments sugars
Takes 4 weeks to form colonies
Only noticed when sealed tubes sitting for 6 months looked contaminated

441
Q

Elusimicrobia
Elusimicrobium minitum
- It is an Ultramicrobacterium

A

Cell volume <0.1 mm3
E. coli = 0.7 mm3
So small it passes through filter normally used to sterilize solutions
When growing rapidly, total cell size has to elongate to accommodate increased ribosome number
National Academy of Science panel concluded life must have at least 0.2 mm diameter
E. minitum diameter 0.17-0.3 mm

442
Q

Chrysiogenetes
Chrysiogenes arsenatis

A

Gram Negative anaerobe
Isolated from reed bed enrichments
Heterotroph
When grown on acetate could only use nitrate as electron acceptor
Can grow on other carbon sources, but requires arsenate as electron acceptor

443
Q

What are the Archaea?

A

Distinct evolutionary lineage – unique from bacteria and eukaryotes
Have characteristics in common with other lineages

444
Q

archaea- similar to bacteria

A

Unicellular, small cells with no organelles
Circular genome
Genes in operons with no introns

445
Q

archaea- similar to eukaryotes

A

No peptidoglycan
DNA replication, repair, association with histones
Transcriptional machinery (promoters, Met initiation, polymerase)

446
Q

Unique to Archaea

A

Cell wall (pseudomurein, sole S-layer)
Ether lipids (found in bacteria but very rare)
Translation (ribosome structure, tRNA sequences)

447
Q

So where are these special bugs?
archaea

A

Originally thought to be confined to most extreme environments
Hot springs, acidic lakes, etc
DNA sampling indicates much more widespread
Soil, lakes, ocean, etc
No spore-formers
No pathogens
Some are commensal (e.g. intestine)

448
Q

Archaeal Phylogeny- phyla

A

Two major: Euryarchaeota and Crenarchaeota
“Korarchaeota” deeply branching phylum
Related to Crenarchaeota
“Nanoarcheota” – based on single species found in 2003
Another potential group of ultrasmall archaea found in 2006
“Thaumarcheota” group proposed in 2008

449
Q

Euryarcheota

A

Largest archaeal group
Found in broad range of environments
Major groups
Halophiles
Methanogens
Thermoplasmas
Hyperthermophiles

450
Q

Halophiles

A

Require high salt concentration for growth
Most can live in saturated salt solutions
35% NaCl, 10x concentration salt water
Face a unique problem – reversal of osmotic pressure
Accumulate ions in cell to balance osmotic equilibrium
K+
Halorhodopsin
Related to rhodopsin that senses light in human eye
Light-driven Cl- pump, accumulates Cl- in cell against gradient
Bacteriorhodopsin
Light-driven H+ pump
Generates Proton Motive Force, completely different than ETS
Most studied: Halobacterium – found in Great Salt Lake, Dead Sea, etc.

451
Q

Methanogens

A

Obligate anaerobes
Sensitive to even trace amounts of O2
Generate CH4
Some from carbon substrates
Many from H2 + CO2 (autotrophic)
Most mesophilic, some thermophiles
Common in anoxic environments
Intestines, wetlands, deep subsurface, wastewater plants
Diverse group

452
Q

How Methanogens led to the internal combustion engine

A

Alessandro Giuseppe Antonio Anastasio Volta
Known for works in electricity
Voltaic Pile – predecessor to the battery
1776 – noticed bubbles rising from disturbed mud in Lake Maggiore
Wanted to experiment with the gas
Voltaic Pistol
Device to capture marsh gas, detonate it
Measured force of explosion
Led to first measurments of O2 in atmosphere
Voltaic Pistol predecessor to internal combustion engine

453
Q

Thermoplasmatales

A

Hyper-acidophilic (pH <2.0)
Some also thermophilic

454
Q

Thermoplasmatales
Thermoplasma

A

Facultative anaerobe (O2 or S electron acceptor)
Found originally in coal refuse piles

455
Q

Thermoplasmatales
Ferroplasma

A

Chemoautotrophs (Fe2+ electron donor)
Found in mine tailings – oxidize pyrite (FeS), produce acid
Tailings = leftovers after ore extraction, very toxic

456
Q

Thermoplasmatales
Picrophilus

A

Optimal growth pH 0.7 (lowest known, like sulfuric acid)
Found in acid hot springs
This bug lives in boiling acid

457
Q

Hyperthermophilic Euryarchaeota

A

Small, unrelated groups
Grow at very high temperatures (>85oC)
Branch close to the root of archaeal tree

458
Q

Pyrococcus furiosus

A

Growth optimum 100oC
Growth maxiumum 103oC
Anaerobic heterotroph
- Produces CO2 + H2, but H2 is toxic to organism
- Uses S to make H2S, gets no energy from reaction
Found in geothermal marine sediments
Enzymes
- DNA polymerase Pfu alternative to Taq
- Some enzymes require tungsten (unique)

459
Q

Crenarchaeota

A

Cultured: genetically diverse hyperthermophiles
Environmental DNA: may be most abundant Archaea in ocean (all temps)
Phenotypically separated based on environment
Terrestrial (hot springs)
Submarine (hydrothermal vents)

460
Q

Terrestrial Hyperthermophilic Crenarchaeota
Sulfolobus (spherical with lobes)

A

One of the most studied (easy to culture)
Aerobic chemoautotrophs (Fe2+, H2S, S electron donors)
Can use organic substrates with aerobic respiration
Found in sulfur-rich hot springs (up to 90oC)

461
Q

Terrestrial Hyperthermophilic Crenarchaeota
pyrobaculum

A

Facultative anaerobes (S, NO3- electron acceptors)
Found in neutral/alkaline hot springs

462
Q

Submarine Hyperthermophilic Crenarchaeota

A

Includes most thermophilic Archaea
Found around deep sea hydrothermal vents
>100oC, 2,000-5,000 m deep

463
Q

Submarine Hyperthermophilic Crenarchaeota
pyrodictum

A

(growth optimum 105oC)
Disc-shaped cells growing as mycelium
Obligate anaerobes
Oxidize organics or H2
S electron acceptor

464
Q

Submarine Hyperthermophilic Crenarchaeota
Staphylothermus

A

(growth optimum 92oC)
Growth pattern resembles Staphylococcus
Ferments proteins

465
Q

Submarine Hyperthermophilic Crenarchaeota
Pyrolobus fumarii

A

Most thermophilic organism known
Can grow at 113oC, survive at 121oC (autoclave)
Autotroph, H2 donor, NO3-/thiosulfate/low O2 acceptor

466
Q

Korarchaeota

A

No cultured isolates
Can culture with other organisms
Only been found in hydrothermal environments
Originally sequenced 16S from Obsidian Pool, Yellowstone
Branch very closely to base of Archaea
May be similar to ancient life

467
Q

Nanoarchaeota

A

Appear to be tiny, parasitic cells on some thermophilic Crenarchaeota
Distinct from other Archaea, but not much else clear about them
Nanoarchaeum equitans (only named species)
Lives on Ignicoccus
1/100 size of E. coli
Very small genome (490 kbp, smaller than Mycoplasma)
Cannot make amino acids, lipids, nucleotides, cofactors
Does have DNA replication/repair machinery
Not clear if it can make it’s own ATP (is this alive?)

468
Q

Thaumarchaeota

A

Newly-proposed phylum
Four species
- Nitrosopumilus maritimus
- Cenarchaeum symbiosum
- Nitrososphaera viennensis
- Nitrososphaera gargensis

All chemolithoautotrophic ammonia-oxidizers
May be important for biogeochemical cycles

469
Q

Nitrosopumilus maritimus

A

in open ocean, cultured

470
Q

Cenarchaeum symbiosum

A

sponge symbiont

471
Q

Nitrososphaera viennensis

A

soil

472
Q

Nitrososphaera gargensis

A

46oC hot spring

473
Q

Archaea have a lot of hyperthermophiles
How do they survive at such high temperatures?

A

lipids
protein
dna
temp limit prob determined by monomer stability
– ATP breaks down quickly at 120oC, unstable at 150oC

474
Q

lipids- archaea hyperthermophiles

A

Composition different so more stable (longer chain, ether linkage)

475
Q

protein- archaea hyperthermophiles

A

Different amino acid composition to make more stable
More densely packed, less floppy parts
More chaperones (aid in folding)

476
Q

dna- archaea hyperthermophiles

A

Reverse Gyrase adds positive supercoiling
Only found in organisms >70oC
Most genomes negatively supercoiled
May have proteins/salts to prevent denaturing

477
Q

viruses

A

Genetic elements need host cell to replicate
DNA or RNA
Replicate independently of host chromosome
Have stable, transmissable extracellular form
Different from plasmids
Formation of extracellular form usually destructive to host cell
Classified based on host
Bacteriophage  viruses that infect bacteria

478
Q

Where do viruses come from? RT

A

Regressive theory – were bacteria that degraded
E.g. Nanoarchaeota

479
Q

Where do viruses come from? COT

A

Cellular origin theory – were plasmids that grew up
Plasmids that transfer are kind of like virus genomes

480
Q

Where do viruses come from? CT

A

Coevolution theory – independent origin
Ancient; evolved with cells from the beginning

481
Q

virus composition

A

Extracellular form = virus particle, virion
Nucleic acid surrounded by protein coat (capsid)
Intracellular form = just the genome
Genome comes in variety of flavors
DNA or RNA
Single or double-stranded
Linear or circular

482
Q

Virion structures

A

Small
Generally 1/100 size bacteria
Small genome
Generally 5,000-200,000 bp
Capsid
Repeating structural protein subunits (capsomers)
Capsomers self-organize
Nucleic acid + capsid = nucleocapsid
Some nucleocapsids surrounded by lipid bilayer
Envelope

483
Q

Virus shapes

A

Rod-shaped- Helical symmetry
Spherical-shaped- Icosahedral symmetry
Complex- Multiple symmetrical parts

484
Q

virus replication Step 1: Attachment (Adsorption)

A

Virion has outer proteins that recognize specific host surface protein (receptor)
Virus proteins in capsid or envelope
Receptors usually perform other necessary function
Virus coopts protein for own use
Can have different stages of attachment through different structures
No receptor, no attachment, no infection
Virion receptor recognizing proteins good targets for antibodies
Antibodies physically block receptor binding

485
Q

virus replication Step 2: Penetration

A

Whole/part of virus enters cell
Chromosome can be injected (e.g. T4 phage)
Particle can be taken in
Envelope fuses with membrane, release particle
Can be multi-stage process
Influenza virus bind receptors, taken in by phagocytosis
Acidification of phagosome alters structure of receptor-binding protein
Hydrophobic portion of receptor-binding protein initiates fusion, escape from phagosome

486
Q

virus replication Step 3: Replication

A

Host cell machinery hijacked – used for viral replication
Viral mRNA made to produce “early proteins”
Mechanism varies
DNA or RNA, single or double-stranded
“Early proteins” carry out replication of viral genome
“Late proteins” expressed
Mainly for making up virion particle

487
Q

virus replication Step 4: Assembly

A

“Late proteins” spontaneously assemble into capsomers
Capsomers arrange themselves around nucleic acid to form capsid
Naked virions done here
Enveloped virions derive membrane from host membrane
Virion receptor-binding proteins in envelope must be put in host membrane first

488
Q

vis replication Step 5: Release

A

Mature virion particles released from host
Usually host cell lyses
Some viruses released from intact cells

489
Q

baltimore classification system

A

Class I: Double-stranded DNA
Class III: Double-stranded RNA
Class V: Single-stranded RNA (Negative)
Class VI: Single-stranded RNA
(DNA intermediate)

490
Q

Bacteriophage

A

Identified for many, many bacteria
Most are naked but with complex structure
Why?
Most well-studied: infect enteric bacteria
E. coli, Salmonella typhimurium
Most common: double-stranded DNA (Class I)
T4, Lambda, T7 (infect E. coli)
Also single-stranded DNA, and RNA (double-stranded, both single-stranded varieties)

491
Q

Animal Viruses

A

Enveloped much more common
Whole virion enter cell

492
Q

Animal Viruses
persistant

A

Virions continually released without cell death
Common for enveloped

493
Q

Animal Viruses
latent

A

Delay between infection and replication
DNA not integrated into host genome
Sporadically enters lytic pathway
Herpes simplex virus (cold sores)

494
Q

Common Animal Viruses
Single-stranded RNA (very common)

A

Rhinovirus
Common cold – respiratory epithelial cells
Rabies virus
Rabies – nerves, brain cells
Influenza viruses
Various
Poliovirus
Poliomyelitis – fecal/oral transmission, infects central nervous system

495
Q

Common Animal Viruses
Double-stranded RNA (very common)

A

Rotavirus
Gastroenteritis in infants – fecal/oral transmission, small intestine cells

496
Q

Common Animal Viruses
DNA

A

(often latent)
Herpes Simplex Virus
Genital herpes, cold sores
Varicella Zoster Virus
Chicken Pox (latent resurgence – Shingles)
Poxviruses
Small pox

497
Q

Smallpox
“Great Pox” = syphilis

A

Double-stranded DNA
Emerged in humans ~10,000 BC
At least 7 deities dedicated to smallpox
End of 1700’s killed 400,000 Europeans a year
5 monarchs
Caused third of all blindness
Two forms
Variola minor – less common, 1% mortality
Variola major – more common, 35% mortality
Airborne transmission most common
1796 – Edward Jenner shows cowpox virus effective vaccine against smallpox
WHO smallpox eradication programs in 1950’s and 1960’s
Last natural case in 1979
Humans are only reservoir – it is now gone from the Earth
Except: two stocks maintained (CDC in Atlanta, VECTOR in Koltsovo, Russia)
One of two eradicated diseases (Rinderpest – cattle virus, 2011)

498
Q

Retroviruses

A

RNA virus with DNA intermediate
Generally enveloped
Two identical single strands and enzymes in capsid
RNA replicated as DNA by Reverse Transcriptase
Very inaccurate  high mutation rate
DNA integrates into host chromosome
Rous Sarcoma Retrovirus (chickens)
First virus shown to cause cancer (oncovirus)
Human Immunodeficiency Virus
Causes AIDS – infects helper T cells
Destroys the immune system  secondary infections

499
Q

Ebola Virus

A

Single-strand negative sense
Enveloped
Persistent
Requires BSL-4 (highest level)
Flu-like onset
Hemorrhagic fever
Blood clots in small vessels
40% bleed from mucous membrane
Death from multiple organ failure
Typical mortality in outbreaks 65-75%

500
Q

Zika Virus

A

Flaviviridae – similar to Dengue, Yellow Fever, West Nile
Icosohedral, enveloped
10 kB (+)RNA genome
7 non-structural and 3 structural proteins

There is no treatment
There is no vaccine (maybe 10 years out)

501
Q

zika transmission

A

Day feeding mosquitos
Sexually
Mother-to-fetus
Severe microcephaly where portion of skull has collapsed
Reduced brain growth
Impacted joints
Based on similar viruses unlikely to impact future pregnancies once virus is cleared (immune after)

502
Q

Coronavirus

A

Positive-sense single strand RNA genome
26-32 kb
5’ methyl cap, poly A tail
Helical symmetry
Enveloped

Club proteins give a “halo” or “corona”appearance under electron microscope
Club proteins function in receptor interaction and membrane fusion

503
Q

Coronavirus epidemiology

A

4 subfamilies of coronavirus
2 naturally reside in birds
2 naturally reside in bats

Respiratory infections in birds and humans
Digestive infections for everything else

7 coronavirus strains infect humans (through animal intermediates)
4 mild, part of common cold pool (200+ viruses, mostly rhinovirus)
3 serious (SARS-CoV, MERS-CoV, SARS-CoV-2)

504
Q

Mimivirus

A

Naked, linear double-stranded DNA genome
Infects amoeba
Discovered in 1992 during Gram Stain
Mistaken for Gram Positive microbe
Capsid diameter 390 nm (second largest)
Bigger than some bacteria
1.2 Mbp genome
Bigger than some bacteria
Genome surrounded by lipid bilayer
Genes for tRNA’s, sugar, lipid, amino acid metabolism
mRNA transcripts in nucleocapsid (DNA replicase, tRNA’s)
Missing Link between bacteria and viruses
Sputnik Virophage
“Virus” of amoeba that requires mimivirus infection to replicate
Essentially, a virus of a virus

505
Q

Groups of human-associated microbes

A

Normal microflora
Indigenous microbiota
Hundreds of species
90% cells on/in human body are microbes

Parasites
Organism living on/in host to detriment of host
Microbial parasites = pathogens

Opportunistic pathogens
Cause disease under unusual situations
Host defenses not present
Likeliness of pathogen causing disease = virulence

506
Q

Terminology

A

Infection
Microorganism present and growing in host
Does not have to cause harm

Disease
Damage to host that affects it’s function

Virulence
Measure of pathogenicity of organism
Can be expressed as number of cells to trigger host response
Colloquially refer to amount of damage done to host

507
Q

Where bacteria interact with their host

A

Anywhere there is an surface
Human body is a conglomeration of microenvironments
Each environment has own moisture, temperature, pH, nutrient availability
Conditions of environment dictate microbes present
Body has lots of mucous membranes
Moist areas exposed to external environment
Microorganisms love these
Attach, possibly penetrate and cause disease
Distinct regions
Skin, oral cavity, respiratory tract, intestines, urogenital tract

508
Q

Bacteria on the skin

A

Skin generally too dry for most bacteria
Most found around sweat or sebaceous glands
Resident vs. Temporary populations
Residents – generally Gram Positive
Staphylococcus (epidermidis)
Propionibacterium (acnes)
Corynebacterium
Acinetobacter (Gram Negative)
Temporary
E. coli and Enterobacter
Common transient from fecal contamination

509
Q

Bacteria in the mouth

A

Moist, warm, nutrient-rich
Bacteria happy
Saliva dilutes nutrients, contains lysozyme (degrades peptidoglycan) and lactoperoxidase (generates toxic oxygen species)
Bacteria unhappy
Some organisms (including methanogenic Archaea) invade gums
Gingivitis, periodontal disease
Most attached to surface in biofilm

510
Q

Progression of dental plaque formation

A

Teeth cleaned
Surface rapidly coated with organic film (saliva)
Initially colonized by Streptococcus
Other bacteria colonize as it thickens
Fusobacterium (filamentous), Borrelia, Actinomyces (filamentous)
Anaerobic species become more common as plaque develops
Bacteria in plaque produce organic acids, decalcify tooth enamel
S. mutans, S. sobrinus sugars  lactic acid

511
Q

Bacteria in the gastrointestinal tract

A

Stomach
Acidity prevents ingested bacteria from reaching intestine
Few can live in stomach itself (Helicobacter pylori)
Duodenum
Still acidic, has lower numbers of bacteria
Jejunum and Ilium
Increased numbers Enterococcus and Lactobacillus
Up to 107 bacteria/g content toward end of Ilium
Large Intestine
Some facultative anaerobes (enterics)
Mostly obligate anaerobes (Bacteroides, Clostridium)
1010 bacteria/g content
Also some methanogens (Archaea)

512
Q

We want bacteria in our intestines

A

Intestinal bacteria:
Produce Vitamin B12 and K
Activate some steroids produced by liver
Produce enzymes that aid digestion
Diet can affect microflora
High meat promotes Bacteroides instead of coliforms and lactic acid bacteria
Bacteroides often protein degraders
Oral antibiotics kill/inhibit gut microflora
Pathogens take over
Clostridium difficile  pseudomembranous colitis

513
Q

Bacteria in the respiratory tract

A

Upper respiratory tract (nose, pharynx/throat)
Whatever is airborne gets trapped in mucous of nasopharynx/throat
Mucous gets shuttled to stomach for disposal
Staphylococcus, Streptococcus common

Lower respiratory tract (trachea, bronchi, lungs)
No resident microflora
Cilia push bacteria up and out
Rest get eaten by alveolar macrophages

514
Q

Bacteria in the urogenital tract

A

Bladder is sterile
Urethra colonized by facultative anaerobes
Escherichia, Klebsiella, Proteus
Can be pathogenic at high numbers
Vagina colonized by acid-tolerant microbes
Weakly acidic
Lactobacillus acidophilus ferments glycogen to lactic acid
Yeasts common

515
Q

How do pathogens get inside us?

A

From a surface
Skin, mucous membrane, intestinal epithelia
Often through wound
Usually specifically adhere to these surfaces
Cell surface proteins, polysaccharide, fimbriae, pili
Most penetrate epithelial tissue
Move to other parts of the body through blood/lymph
Initial infection usually localized but can spread
Bacteremia – bacterial growth in blood stream itself

516
Q

Virulence Factors

A

Bacterial products that help pathogen enter host more efficiently or stay in host longer
Often extracellular enzymes
Hyaluronidase (S. pyogenes, S. aureus, C. perfringens)
Breaks down intercellular matrix between host cells
Streptokinase (S. pyogenes)
Breaks down fibrin clots
Used by host to limit bacterial spread
Coagulase (S. aureus)
Forms fibrin clots
Cloaks/protects cells from host immune response

517
Q

Toxins
Exotoxins

A

Extracellular proteins released by some pathogens
Cytolytic toxins
Cause host cells to lyse
E.g. beta hemolysins
A-B toxins
Have components that bind and enter host cells
E.g. botulinum toxin, tetanus toxin
Block release of neurotransmitters
E.g. diptheria toxin
Damage heart muscle/neural tissue
Superantigen toxin
Trigger massive immune response

518
Q

Toxins
Enterotoxins

A

Exotoxins that affect the small intestine
Secretion of huge amounts of fluid
Diarrhea and vomiting
Produced by intestinal pathogens, food poisoning pathogens
Can get food enterotoxins without bacteria being present
Most well-known is Cholera toxin (V. cholerae)
A-B toxin
Cause epithelial cells pump out Cl-, prevent import Na+
High salt buildup outside of cell  water efflux out of cell
Benefit isn’t clear, possible the bacteria is screwing up colonization
Increases cAMP which bacteria eats, but also causes water loss
Death by dehydration

519
Q

Toxins
Endotoxins

A

Shed LPS from Gram Negative bacteria that cause toxic effect
Usually released when cells lyse
Polysaccharide chains make molecule soluble
Lipid portion toxic
Lead to:
Fever (“pyrogenic”, raise host body temp)
Diarrhea
Inflammation
Immune response
Rarely fatal unless in high doses
Non-bacteriolytic antibiotics

520
Q

Cellular differences between Eukarya and Bacteria/Archaea

A

Eukarya always have membrane bound nucleus
Other organelles vary
Almost all eukaryotes have mitochondria
Where did mitochondria come from?
Photosynthetic eukaryotes have chloroplasts
Where did chloroplasts come from?
A few microscopic eukaryotes have hydrogenosome
Oxidizes pyruvate, produces H2
Only found in organisms that carry out fermentation
Likely derived from mitochondria

521
Q

Types of microbial Eukarya

A

Traditionally divided in animals, plants, fungi and protists
DNA suggests protists divided into multiple distinct lineages

522
Q

Diplomonads

A

Most exist as paired cells, each with 4 flagella
Lack mitochondria and Golgi

Giardia lamblia
Causes giardiasis
Ingestion of cysts
Develop into trophozoites
Active, replicating form
Swim around intestine
Causes explosive diarrhea, excessive sulfurous gas, nausea

523
Q

Trichomonads

A

Anaerobic, flagellated cells
Do not form cysts
Lack mitochondria, have hydrogenosomes

Trichomonas vaginalis
Causes Trichomoniasis
Most common protozoan pathogen in developed countries
5 million cases/yr in US, 160 million worldwide
Sexually transmitted urogenital disease (direct, no cysts)
Men usually asymptomatic
Women have “strawberry cervix” – punctate pattern on surface
Increased susceptibility to HIV, cervical cancer

524
Q

Protozoa

A

Various separate lineages traditionally grouped together
Single-celled, lack cell walls
Feed by engulfing particles (phagocytosis)
Most motile
Classified by motility method

525
Q

Mastigophora
Flagellates

A

Many free-living in soil/water
Some parasites
Some have chloroplasts (e.g. Euglena)
Likely most ancient group of protozoa

Trypanosoma brucei – African Sleeping Sickness
Spread by Tsetse Fly
Stage 1 – hugely swollen lymph nodes, fever, ache
Stage 2 – parasite crosses blood-brain barrier
Confusion, fatigue, day-time slumber, night-time insomnia
Parasite produces tryptohol – induces sleepiness in human

526
Q

Mastigophora
Flagellates
2

A

Trypanosoma cruzi – Chagas Disease
Spread by Reduviid bugs (“Kissing Bugs”)
Hide in crevices during day
Come out at night to feed on peoples faces
Attract to CO2 among other things  lips
After feeding, they defecate
People rub feces into bite
Acute stage – fever, rash, diarrhea, etc.
Chronic stage – 60-80% asymptomatic
Rest – life-threatening heart/digestive disorders
13% stillborns in Brazil
Leishmania - Leishmaniasis
Spread by Sand Flies
Huge skin ulcers, spleen/liver damage

527
Q

Ciliophora
Ciliates

A

Motile with cilia at some stage of life cycle
Cilia – shorter flagella in large numbers
Can use cilia for feeding – sweep food into “oral groove”
Have two kinds of nuclei
Micronucleus
Diploid – used for reproduction
Macronucleus
Polyploid – used for mRNA/protein
Most free-living in soil/water (e.g. Paramecium)
Some anaerobes in rumen
Some invertebrate parasites

528
Q

Sarcodina
Amoeba

A

Motile through amoeboid motion (crawling)
Extension of pseudopod, cell flows into pseudopod
Exact mechanism unknown
Maintain osmotic balance through Contractile Vacuole
Vesicle fills with water, contraction ejects water into surroundings
Under unfavorable conditions, can form cyst
Common in soil/water
Some parasites (mouth, digestive tract)
Entamoeba histolytica – amebic dysentery
Ingestion of cysts, trophozoites in intestine
Damage intestinal wall – bloody diarrhea, spread to organs

529
Q

Foraminifera

A

Originally classified with Amoeba, now own phylum
Uses pseudopods for locomotion, feeding
Most less than 1 mm diameter
Largest over 6 cm (2 inches)
Fossils from Cambrian era up to 15 cm
Size due to production of “test” (shell)
Different compositions depending on species
Carbonate, silica, organic material
Test usually chambered, with organism occupying last few chambers
Hole(s) open to ocean for pseudopods
Some anterior chamber can be colonized by algae/cyanobac

530
Q

Apicomplexa
Sporozoans

A

No motile adult stage
Obligate animal parasites
Form sporozoites (spore-like cells) for transmission
Plasmodium falciparum, Plasmodium vivax
Cause malaria – infect red blood cells
Fever, aches, anemia
Transmitted by mosquitoes
500 million cases/yr (2 million deaths)
Cyclospora
Fecal-oral cyst transmission (contaminated fruits/water)
One of causes for “Traveler’s Diarrhea”
Cryptosporidium
Fecal-oral (water)
Short term diarrhea
Fun fact: rare in that mitochondria don’t have DNA

531
Q

Toxoplasma gondii

A

Two stage life cycle
Sexual stage – intestines of cats, produce cysts
Asexual stage – warm-blooded animals
Mice (which is eaten by cat), birds, humans
Both stages, organism lives in cellular vacuole
Contracted by cat feces, contaminated food (pork)
Evades immune system
Causes toxoplasmosis in humans
Acute – aches, swollen lymph nodes
Latent – cysts persist in muscle, nerve tissue
Approximately 1/3 world infected (10-12% US)

532
Q

Toxoplasma gondii
2

A

T. gondii induces behavior changes in mice
More adventurous, less fearful (dopamine)
Some seek out places marked by cat urine
Increases likelihood mouse eaten by cat
T. gondii wants this

T. gondii linked to mental disorders in humans
Anxiety, depression, schizophrenia
Exact reason very unclear
By-product of behavior modification system
Cysts in nervous tissue early in development
Inducing latent human genes

533
Q

Fungi

A

Chitin cell wall, produce spores
Usually classified on spore/spore-containing structures
Tight lineage
Ascomycetes – e.g. yeasts (Saccharomyces)
Basidomycetes – e.g. mushrooms (Agaricus)
Zygomycetes – e.g. bread molds (Rhizopus)
Multiple cell forms
Single cell – yeast form
Filaments – hyphae (mycelium)
Many can switch between forms
Most terrestrial, some aquatic
Detritivores – aerobic heterotrophs, significant degradation organisms
Some plant/animal/human pathogens
Candida albicans – oral/genital infections (“thrush”, candidiasis)

534
Q

Slime molds

A

Separate lineage, characteristics of fungi and protozoa
Found on decaying plant matter, mainly feed on bacteria
Two main groups
Acellular (plasmodial) – e.g. Physarum
Cellular – e.g. Dictyostelium
Acellular slime molds
One gigantic, multi-nucleate amoebic cell (can be over meter in diameter)
Cellular slime molds
Separate amoebic cells
When starved, both types form sporangia (spore-containing fruiting bodies)
Cellular slime molds – multiple cells group together to form essentially new organism
Spore germination
Acellular – form swarmer cells that fuse into plasmodium
Cellular – form separate cells

535
Q

Algae

A

Oxygenic photosynthetic Eukarya
Some capable of heterotrophy in dark
Chloroplasts – chlorophyll a, other pigments
Mainly classified on accessory pigments
Chlorophyta – green algae
Rhodophyta – red algae
Diatoms
Abundant in aquatic/moist environments
Microscopic or macroscopic (seaweed)
Unicellular or colonial
Dinoflagellates – related to Ciliophora
Free-living or symbiotic
Blooms cause Red Tide

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