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MICR 2420 > INTRO PHYLOGENY > Flashcards

INTRO PHYLOGENY Flashcards

1
Q

Linnaean taxonomy

A

system for naming and animal classification

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2
Q

kingdoms in linn. taxonomy

A

animal
plants
minerals

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3
Q

hierarchy for classifications

A
  1. kingdom
  2. phylum
  3. class
  4. order
  5. fam
  6. genus
  7. species
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4
Q

linnaeus

A

-linnean taxonomy
-3 kingdoms = animal, plant, mineral
-created hierarchy naming system

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5
Q

haekal

A

added phylum
added monera, protista kingdoms

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6
Q

whittaker

A

added fungi kingdom
superkingdom level (euk and prok)

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7
Q

woese

A

father of molec phylogeny
ribosomal rrna bet organisms
archaea = extremophile prokaryotoes
revolutionalized way we classify life

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8
Q

margulis

A

endosymbiant theory

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9
Q

1st event in endosymbiant theory

A

ancestral eukaryote consumes aerobic bacteria = mitochondria
=modern day heterotrophic eukaroyote

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10
Q

2nd event in endosymbiant theory

A

early euko consumes photosythetic bacteria
=choloroplasts
=modrn photosynthetic eukaryote

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11
Q

what can we use rRNA for?

A

organism identity and phylogeny

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12
Q

what are the 3 main branches in the ToL?

A
  1. bacteria
  2. archea
  3. eukarya

basically domains

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13
Q

what makes th ToL unique?

A

based on rRNA sequencing instead of morpho traits for classification

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14
Q

predecessor to mitochondria? chloroplasts?

A

proteobacteria and cyanobacteria

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15
Q

what kingdoms are microbal?

A

fungi, protista, bacteria and archaea

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16
Q

what are harmful bacteria called

A

pathogens

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17
Q

cells walls of bacteria contain

A

peptidoglycan (sugar and AA)

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18
Q

bacterial morphology

A
  1. coccus
  2. bacillus
  3. coccusbacillus
  4. vibrio
  5. spirrilium
  6. spriochete
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19
Q

archaea

A

extremophiles
pseudopeptidylcan cell wall
not human pathogens

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20
Q

are there archaeic human pathogens

A

nope

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21
Q

2 types of protisists

A

algae and protozoa

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22
Q

algea cell wall

A

cellulose

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23
Q

are

are algae photosynthetic

A

yes

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24
Q

protozoas move via?

A

cilia and flagella

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25
Q

ex

ex of protozoa

A

tapeworm

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26
Q

types of fungi

A

molds or yeasts

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27
Q

fungi cell wall

A

chitin = not photosynthetic

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28
Q

mold vs yeast

A

mold
=multi cell
=decomp
=pharmacy penicilin
long filaments

yeast
=uni
=gonadal infections
=oral flush

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29
Q

what causes oral flush and gonadal infcetions

A

yeast (fungi)

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30
Q

properties of virus

A

acellular
have RNA or DNA but never both
(protein and genetic material)
hijack host cell mechens

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31
Q

how do ABs work

A

some ribosomal function by taregting ceullar part of outer envelope

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32
Q

what is brightfield imaging

A

dark image on bright background

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33
Q

simple stain vs diffrential stain

A

simple = adds colour to cells present only and not surrounding tissues
differential = stains specific kind of cell but not other

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34
Q

example of diffrential and simple stain

A

diffrential = gram
simple = methylene blue

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35
Q

what traits do bacteria and archaea share

A

-70s ribosome
-asexual reproduction
-unicellular
-complex cell walls
-circular genome
-no membrane bound organells

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36
Q

how is morphology preserved in prok cells?

A

via cell wall

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37
Q

role of cell wall

A

protects against turgor pressure changes

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38
Q

isotonic vs hypertonic vs hypotonic solution

A

no net movement of h20
h20 exits cell = membrane shrinks away from cell wall
h20 move into cell = cell wall counteracts to stop swelling

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39
Q

how is DNA stored in prokaryotes

A

in nucleiod region
DNA = unbound, circular, haploid

Can also be found in plasmids = small, circular double stranded molecules

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40
Q

important thing to remember about PM in bacteria and archea?

A

bacteria = phospholipid bilayer (ester bond that links fatty acids to glyercol/phosphate)
archaea = tetraether monolayer (ether bonds that link branched phytanyl side chains to glycerol and/phosphate)

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41
Q

how is tetraether monolayer different?

A

rigid
structure
higher melting temp
less permeable
ether bonds
branched phytanyl side chain

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42
Q

which bacteria has bacteriorhodopsin

A

h salinarum = in its PM

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43
Q

bacteriorhodopsin

A

light activated proton pump
phototrophic

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44
Q

modes of ETC

A

lithotrophic = e donor is inorganic
phototrophic = light is energy source
heterotrophic = e donor is organic

all contribute to the PMF

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45
Q

what is PMF

A

proton motive force cretaed by ETC
H gradient across membrane = stored energy =work done inside cell

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46
Q

membrane transport mechanism types

A

simple diff
facilitated diff
active transport

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47
Q

how does the ETC create energy for the cell?

A

PMF (H gradient created)
H enter cell which drives ATP synthesis

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48
Q

types of active transport

A

coupled
atp binding casette transportters
group translocation

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49
Q

explain ATP synthesis

A

atp synthase uses e gradient to convert ADP and Pi to ATP

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50
Q

what does it mean that the PG is an isolated sacculus?

A

the PG is considered a single giant macromolecule that encases the entire bacterial cell

Basically when you remove all other cellular components from the cell wall, there is a purified layer of PG that helps maintain cell shape

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51
Q

Do all bacteria have a PM with phospholipid bilayers?

A

Not hyperthermophilic bacteria

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52
Q

who has phospholipid bilayer PM?

A

bacteria except hyperthermophilic
some archaea
all eukaryotes

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53
Q

what is the type 3 secretion system

A

found in gram neg bacteria
needle like complex that injects effector proteins into host cells
important for pathogenic bacteria to manipulate host cells

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54
Q

what is LPS

A

lipopolysaccaride
key part of the outer membrane of gram neg cell walls

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55
Q

components of LPS

A

lipid a
core polysacc
o side chain

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56
Q

role of LPS

A

endotoxin / virulence factor
= fevers, hemorraging anf septic shocks

permeability barrier to hydrophobic molecules

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57
Q

what part of LPS is a virulence factor

A

lipid A = endotoxin (which is a type of virulence factor)

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58
Q

kaufmann white scheme

A

serotyping method for classifying salmonella based on LPS and surface antigens

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59
Q

acid fast staining rxn

A

staining method for acid fast bacteria that cant be stained with normal technique

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60
Q

acid fast bacteria example

A

myobacterium

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61
Q

why cant myobacterium be stained normally

A

weird cell wall lipids
weird sugars
resistant to immune clearance
waxy layer of mycolic acids

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62
Q

Role of s and capsule layers

A

part of the cell wall of bacteria or archea
-virulence factors
-make biofilms bc allow cells to stick to their surface
-protect against dessication (removal of moisture)

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63
Q

what helps biofilm attachement happen?

A

pili
= short protein filaments that are involved in attachment of other cells

capsule layer and LPS on cell walls

fimbraie

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64
Q

fimbraie vs pilli?

A

fibraie
= short
=attach to cells

pilli
=long
=less numerous
=dna transfer

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65
Q

bacterial conjugation

A

type of horizontal gene transfer

transfer of genetic material from donor to recipient
done via sex pilli

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66
Q

what drives the flagellar motor

A

proton motive force

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67
Q

where is the flagellar motor anchored

A

betw nacterial and archeal PM

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68
Q

flagellar motor

A

embedded in PM and rotates the flagellar filament which is made up of flagellin proteins that have h-antigens embedded in it

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69
Q

describe how flagellum moves

A

switching between running (ccw) and tumbling (clockwise)

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70
Q

biased random walk

A

direction after tumbling is random but over net progression either towards attractant or away from repellent

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71
Q

quorum sensing

A

intracell communication meche
coordinate gene expression based on population density

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72
Q

lux paradigm system

A

example of quorum sensing

  1. luxI protein synthesizes AI (autoinducer)
  2. when quorum level reached, AI bind to LuxR (response regulator)
  3. AI - LuxR complex binds to Lux promoter region on DNA sequence = Transcription regulators activated
  4. gene for biolumincenece activated
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73
Q

how is quorum sensing different in gram positive bacteria.

A

instead of AI, they release quorum sensing peptides that bind to response regulators instead

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74
Q

agr quorum system

A

quorum system in staphylcocci species
used to regulate expression of virulence factors based on pop density

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75
Q

key thing that makes biofilms bad

A

highly resistant to antimicrobials via immune response

76
Q

biofim

A

communities of bacteria surrounded by extrcellular polysacc matrix

77
Q

symbiosis

A

long term interaction/association between 2 different species

78
Q

types of microbial symbiotic associations

A
  1. mutualism
  2. commenalism
  3. parasitism
  4. amenalism
  5. synergism
79
Q

mutualism example

A

both benefit, cant live independently
lichens = fungi and algae growing together in complex layered stucture
biofilms = bacteria and archea

80
Q

synergism example

A

both benefit but can grown independently
-colon bacteria ferment, which releases h2 and co2
-methanogens can convert to methane and gain energy and bacteria get ferment products removed

81
Q

commenalism

A

one benefits, other is neutral

-beggiatoa bacteria oxidize H2S for energy which allows other bacteria to grow

82
Q

amenalism example

A

one benefits, other harmed

-streptomyces bacteria secretes antibiotics that lyse other species for food

83
Q

parasitism

A

parasite benefits at the expense of other host
oblig for parasite

L pneuomphila parasite for amoebas or macrophages in humans

84
Q

what is in lichens

A

fungi = provide minerals
algae = provide carbon

85
Q

is paratism specific?

A

yes

86
Q

which interaction is non specific

A

amenalism

87
Q

syntrophy

A

2 microbe species interaction where they break down a single substrate

88
Q

example of syntrophy

A

methanobacillus omelianskii and syntrophomanus

89
Q

endosymbiosis

A

organism living inside anothers cell or body

90
Q

Mycorrhizae

A

type of mutualistic relationship
fungae take over roots and their hypae = more nutrient absorption
fungae get sugars from plants

91
Q

rhizobia and legumes

A

bacteria and legume plants
mutualistic
nodules formed on roots = n2 fixation
plants get N and bacteria gets sugars

92
Q

explain rumen microbes

A

plant fibre broken down into cellulose by fungi in rumen
cellulose broken down into sugar, h2 and co2 by bacteria
h2 and co2 taken by methanogens and converted into methane

93
Q

what are methanogens

A

type of archea

94
Q

why are cow diet changes harmful maybe

A

diet change = change # e coli 0157 = illness in humans

95
Q

evidence of gut microbiota comes from

A

germ free mice

96
Q

hygiene hypothesis

A

theory as to why there are autoimmune diseases in developed countries

reduced exposure to pathogens at early age = underdeveloped or disregulated immune system that FINDS things to target in body

97
Q

commensal organisms

A

microbes usually found at non sterile body sites that dont cause harm

98
Q

why is commensal def incorrec sometimes?

A

host and microbe interactios vary
can be mutualistic or patho depending on immune system or the dyanmics of community

99
Q

microbiota vs microbiome

A

biota = all micro
biome = genes and products and micro

100
Q

opportunistic infection

A

infection caused by microorganisms that typically do not cause disease in a healthy host with a normal immune system.

101
Q

common bacteria found on skin

A

gram +
staphylococcus epedermis

102
Q

most common infection site humans

A

oral and resp tracr

103
Q

bacteria found in mouth infants

A

infants:
1. neisseria -ve cocci
2. Streptococssu and lactobacillus +ve rods

104
Q

bacteria found in mouth older

A

prevotella and fusobacterium in gums
S. mutans in tooth enamel

105
Q

nose and nasophrynx bacteria

A

bacillota and actinmyecota

106
Q

which is better at keeping us healthy

A

some s eperderimis strains

107
Q

lung bacteria

A

anaerobic
p. aueroginosa

108
Q

sterile organs

A

bladder and kidneys

109
Q

what causes Utis

A

S eperdermis in urethra

110
Q

protection from utis

A

lactobacillus
which loves acidic secretions

111
Q

bacteria in stomach

A

h. pylori = in protective mucus = gastric ulcers

112
Q

what can cause intestinal diease

A

hypoclordyia = less stomach aciditiy
= reduced defense barrier

113
Q

anaerobes : aerobes ratio in lower intensive

A

1000: 1

114
Q

most imp microbial ecosystem

A

colon

115
Q

function of gut microbe

A

immunity
energy extraction from food
pathogen control
metabolite made
intestinal function increase
toxin removal

116
Q

ways to get good microbe

A

vaginal delivery
bF
environment interaction

117
Q

ways to weaken gut microbe development

A

c section
formula feeding
excesive sanitation
maternal ABs
chem preservation of food
indoor living

118
Q

whats the priority goal of healthy gut microbiome

A

diversity

119
Q

why do we want diverse gut microbiome

A

healthy ecosystem
balance
functional redundancy = higher gene count
resistance to damage

120
Q

missing microbiota hypothesis

A

loss of microbiota over generations is normal but recent changes in lifestyle have added to this loss by alot by decreasing diversity
=chronic diease impacting immune system and development

121
Q

examples of nocosoimal infections

A

MRSA
VRE

122
Q

examples of opportunisitc infections

A

S. aureous = ear and blood
s. pneuomoniae = lungs
e coli

123
Q

explain how dysbiosis can cuase diseases

A

antibiotic therapy
=chnage in git community
=health issues
=bf regularlis
=c difficile

124
Q

how does the microbiota protect itself

A
  1. competitive exclusion
    2 environmental mod
  2. host stimulation = increase cytokines immune system
  3. direct pacification => inhbit virulence factor
125
Q

obesity and the gut

A

assciated with a less diverse microbiota
increase inflamm = loss of mircobe and more pro inflamm prodicuing LPS

126
Q

germ free animals

A

low immunity
low CO
more kcal for energy
thin intest walls with low villi
enlarged ceca
odd behaviour
misshaped mitochondria

127
Q

what keeps us healthy despite exposure to pathogens

A

nonspeficifc innate immune defences

128
Q

examples of NIIF

A

physical barriers
mech barriers
microbiomes
chem barriers

129
Q

koch’s postulates

A

does this pathogen cause disease?

  1. MO in diseased orgo but not healthy
  2. isolate the MO and grown
  3. MO introduced to healthy orgo
  4. MO reisolated from exp host and checked if same as the original causation agent
130
Q

tropism

A

specificity of a virus to infect a certain type of host tissue
determined by the ability to bind to certain Rc

131
Q

viruses

A

acellular
obligate intracellular organisms
dependent on a host cell
generally comprise of risk group 4 agents

132
Q

components of viruses

A

genetic material = DNA or RNA
capsid = protective coat
envelope = bilayer obtained from host
spike proteins

133
Q

why are viruses important

A

impact disease/well being
development of mbg and biotech
evolution via changes in gene expression

134
Q

how do viruses get enveloped?

A

via budding process from host cell

135
Q

viral structure types

A

helical
icosahedral
bindal/complex symmetry
irregular

136
Q

classification of viruses

A

1, nature of genome,
2. capside symmetry
3. envelope
4. viral particle size
5 host range

baltimore classifcation scheme

137
Q

baltimore classification scheme

A

classfies based on genome and mRNA relationship
1. ssDNA
2. dsDNA
3 dsRNA
4 +ssRNa
5. -ssRNA
6. +ssRNA-RT
7. dsDNA-RT

138
Q

+ve vs -ve sense

A

+ = translated as soon as enters cell
- = replicated into +ve then translated

139
Q

retrovirus

A

DNA/RNA comverting virus
ssRNA retrovirus

140
Q

life stage of a virus

A

A PUB ARM

attachement
penetration
uncoating
biosynthesis
assembly
release
maturation

141
Q

life cycle of bacteriophage

A

lytic and lysogenic

142
Q

what allows phages to recognize host

A

tail fibres

143
Q

lytic cycle

A

rapide phage replication
lyses and kills host

144
Q

lysogenic cycle

A

intgrates inot DNA genome and dormant

145
Q

phage culture systems

A
  1. batch culture in liquid
  2. isolated plaques on bacterial lawn agar plates
146
Q

cyticidal effects

A

clearing of the host cell

147
Q

HIV Life cycle

A
148
Q

covid life cycle

A
149
Q

what allows hiv to bind to the host

A

reverse transcriptase

150
Q

hiv needs to be?

A

dna for intergration into host cell genome

151
Q

how can we measure virulence

A

infectious dose (ID50) and lethal dose (LD50)

152
Q

infectivity is proportional to

A

inversely proportional to ID50

153
Q

a high infectivity would mean?

A

low ID50

which means that less particles required to infect 50% of the population which means high infectivity

154
Q

limitations to kosch postulates

A

impossible for human only pathogens
super-antigen mediated disease
opportunistic patho
dormancy/latency
polymicrobial diseases
great plate anomaly
exclusively human pathogens

155
Q

how does h pylori cause disease

A

releases urease which neutralizes stomach acid = mucin lining on epi cells liquifies and bacteria goes thru it

156
Q

EHEC

A

strain of bacteria that produces shiga toxins = intestinal issues damage

ex. e coli O157:H7

157
Q

apply Kochs molecular postulates to EHEC

A
  1. EHEC causes diarrhea and inflamm while non pathogenic e coli strains do not
  2. Removal of genes that code for shiga toxins = reduced ability to cause disease
  3. adding the gene back into the genome will cause the EHEcs ability to make disease again
158
Q

how to be a good pathogen

A
  1. get to host
  2. get inside host
  3. defeat immune system
159
Q

how can pathogens increase breaking in

A

adhesins (pili, capsules, LPS, viral coat and envelope proteins)

degradative enzymes
physical health breakdown
indwelling device

159
Q
A
160
Q

what are some characteristics of a effective pathogen?

A

biofilm
intracellular pathogens
intracellular pathogens of immune cells
cell wall structures (LPS, O-anitgen)
acid fast cell wall

161
Q

example of a intracellular pathogen

A

salmonella containing vacuole

162
Q

types of immunity

A

innate
-birth
-non specific
-1 line defense
-no memory

adaptive
-18 months
-specific
last line defsense
memory

163
Q

components of immune system

A
  1. proteins ; antibodies and cytokines
  2. cells ; macrophages, t and b cells, neutrophils, monocytes
  3. vessels ; lymphatic sysyetm blood, mucous
164
Q

extravasation

A

immune cells leak out of circulatory vessels to tissues

165
Q

epitope

A

part of an antigen that is recognized by antibodies and trigger immune response
antigenic determinant

166
Q

what binds to immune cell surfaces

A

antigen

167
Q

what binds to immune cell

A

cytokine

168
Q

how does a phagocyte know to bind to a pathogen?

A

Pattern Regocnition Receptors (PRR) on phagocyte binds to Microbe associated molecular patterns (MAMPs)

169
Q

what is a barrier to phagocytosis

A

virulence factors

170
Q

what binds to antibodies

A

epitope

171
Q

how can pathogens avoid phagocytosis

A
  1. antigen mimicry (mimic the host = hard to recognize)
  2. capusle characteristic (slippery or too big)
172
Q

give an example of immunopathogenesis

A

t. bacillie inhaled and goes to alveoli
multiply
immune cells form barrier = granuloma
granuloma breaks down = escape
= rapid multiply
=mmore tubercles

173
Q

how to escape the immune response

A
  1. avoid phagocytosis
  2. exploit phagocytosis
  3. antigenic variation
174
Q

b cells

A

make antibodies

175
Q

t cells

A

control immune response ad kill infected host cells

176
Q

adaptive immune system

A
  1. memory from previous exposure
  2. antigen specific
  3. tolerance of microbiome in body sites
    4.
177
Q

key players in innate immunity

A

phagocytosis and antigen presenting cells

178
Q

t lymphocytes

A

coordinate and regulate (T helper, T reg)
cell -mediated immunity by destroying infected cells (T cytotoxic)
differentiate into memory cells

179
Q

b lymphocytes

A

make plasma cells which turns into antibodies
memory cells

180
Q

what does acquired immunity always trigger?

A

b cell activation
= plasma cells produced
=antibody secretion

t cell activation via antigen [presentation

181
Q

types of antibodies

A

IgG
IgM
slgA

182
Q

agglutination

A

antibodies bind to antigen on particular surfaces = clump together

183
Q

what type of AB agglutinates alot

A

igM

184
Q
A

MICR 2420 (4 decks)

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