Microbiology Exam 3 Flashcards
(115 cards)
1
Q
Lederberg 1946
A
Used auxotrophic strains of E. Coli to study gene transfer
Had to have direct contact for gene transfer
Said it was sexual reproduction which is wrong, it was conjugation
2
Q
Conjugation
A
DNA is transferred from one cell to another cell
Needs direct contact
Cells are connected by pilus structure
DNA transfer is directional donor cell to recipient cell
3
Q
Plasmid
A
Replicate independently from the bacterial chromosome
4
Q
F-plasmid
A
Has genes so it can replicate independently
Has origin of replication
Has genes (tra region) for conjugation to occur
5
Q
What happens during conjugation?
A
F+ pilus connects to F- cell
F plasmid is replicated by rolling circle replication
Single strand DNA is transferred to the F- cell through the pilus
Takes about five minutes. Recipient cell now becomes F+
6
Q
F plasmid
A
Is what is incorporated into the E. Coli chromosome
Longer cells are in contact, more DNA is transferred
Technique is used to help map E. Coli genome
7
Q
Hfr strain
A
High frequency of recombination
Can transfer DNA to recipient strand
8
Q
What happens of some F plasmid DNA and some chromosomal DNA from the E. Coli strain is transfered?
A
Will not be Hfr if it does not have the entire strain
9
Q
Should auxotrophic strain be donor or recipient strain?
A
Recipient strain
So it initially won’t grow unless they acquire gene from the other strand
10
Q
Eukaryotic cells and how they are chimeric?
A
Contain bacterial genes and archaeal genes and genes unique to eukaryotes
11
Q
Endosymbiosis
A
Mitochondria and chloroplasts arose from symbiotic relationship of a bacterial cell living inside a larger host cell
12
Q
Evidence for endosymbiosis
A
DNA sequences via mitochondrial genes
Are most similar genes of alpha-proteobacteria (Gr-)
Chloroplasts genes are most similar to cyanobacteria
13
Q
Proteobacteria genomes
A
~2-4 mbp in size
14
Q
Human mitochondrial genome
A
~17,000 bp
15
Q
Mitochondrial genome
A
Very few protein encoding genes
Most genes- tRNA, rRNA molecules
Human mitochondria has 13 protein encoding genes
Genes encoding mitochondrial proteins –> most migrated to nucleus
16
Q
Why is it safe to take antibiotics that target the mitochondrial genome of bacteria?
A
They impact the mitochondrion ribosomes but they only have 13 protein encoding genes so therefore it is safe to take
17
Q
Where do eukaryotic cells get their central dogma processes and their metabolic genes/membranes?
A
Central dogma processes come from archaeal cells
Metabolic genes/membranes come from bacterial cells
18
Q
Serial endosymbiotic hypothesis of evolution of eukaryotic cell
A
Eukaryotic cells rose from a nucleus bearing line of archaea. This would explain the central dogma of cells have the archaea origin
Organelles via symbiosis. Genes were transferred to the nucleus
19
Q
Issues with the serial endosymbiotic hypothesis of evolution?
A
Membrane lipids
20
Q
Symbiogenesis hypothesis
A
Eukaryotic cells arose from a symbiotic relationship of a bacterial cell (H2 producing) and an archaeal cell (H2 consuming)
Bacterial cells is precursor of mitochondrial
Nucleus envolved after genes for membrane synthesis were transferred from bacterial genome to the archaeal genome
21
Q
Nature paper
A
Culture independent studies in artic ocean
Found new group of organisms called the lokiarchaeota
22
Q
Lokiarchaeota
A
Noticed within these organisms there was 36 proteins that formed a single phylogenetic group with eukaryote
23
Q
ESP
A
Eukaryotic signature proteins
Could potentially be an ancestor of eukaryotes (archaeal ancestor of eukaryotes)
24
Q
Secondary endosymbiosis
A
Photosynthetic eukaryotes which diverged from green and red algae
Eukaryotic cell incorporated algae to acquire photosynthetic processes
25
Dinoflagellates
Engulfed red algae to get photosynthetic properties
26
Euglema
Green algae with ancestors of chloroplasts
27
Protists
Very diverse group
Single cell microbes
photosynthetic, non photosynthetic
28
Streamwater
Contains microbes
Eukaryotic microbes
Example is giardia
29
Giardia
Intestinal pathogen
Not treatable with antibiotics
Contains 2 nuclei that lacks mitochondria and chloroplasts
Produces cysts that are resistant to chlorination
30
Typamosomes
African sleeping sickness
transmitted by a fly which goes into the bloodstream and can spread to the CNS
31
Euglena
Broad class of protists
Photosynthetic ones and no photosynthetic (chemoorganotrophs--> get energy by ingesting bacteria) ones
32
Paramecium
2 nuclei: macro and micro-nuclei
Genome size is > 40,000 genes
33
Relationships of paramecium
Can be hosts of endosymbiotic bacteria, archaea and eukaryotes
Many different types of symbiotic relationships with other protists
34
Dinoflagellates
Acquired chloroplasts--secondary endosymbiosis of red algae
causes red tides--occurs in warm polluted waters--toxic species produce a neurotoxin that can kill fish and other organisms in the area
35
What disease has killed more people than other disease?
Malaria
36
What causes malaria?
Caused by an organism called plasmodium which is a parasite
Not treatable with antibiotics
There are four types that cause malaria
Has a very complex life cycle
Is transmitted by female anopheles mosquitoes
37
Life cycle of plasmodium
1. Human is bit
2. Releases sporozoites into the body that are removed from blood by liver
3. Become bigger and form a structure called schizont which segment into smaller cells (merozoites)
4. Merozoites leave liver and infect RBC's
Within RBC's they replicate. Get fever, chills, weaker at this point
5. RBC's undergo meiosis to produce gametocytes. At this point mosquito can take up gametocytes
6. Gametes mature there. Fertilization of gametes in mosquitoes. Will develop sporozoites and lifecycle continues
38
Prevention for malaria
To have universal access to treatments and preventions even as the amount of cases reduces. Make sure all at risk populations have access to preventions and treatments
All countries must be able to upgrade their surveillance of cases. This way the cases can be tracked and interrupt the transmission
Investigating and clearing cases
39
Vaccine prevention of malaria
Not a one size fits all because of antigenic variation that is great
Life cycle also is complex and makes the vaccine development hard
Disease also does not affect first world countries
There is a new malaria vaccine that has shown being partially effective with a 30% reduction in hospitalizations
40
Diatoms
Cool looking
cell walls contain silica with proteins and polysaccharides
41
Yeast
would be a eukaryotic fungi (chemoorganotrophs)
42
Fungi
Have important symbiotic synthesis with plants
Help plants to acquire nutrients, minerals from the soil
Mineral cycling/nutrient cycling because of their role in decomposition of plants and animals
Can study cancer by looking at their cell division (they don't get cancer but understanding how cell division works can help with understanding what goes wrong in cancer when you compare cancer to their cell cycle)
43
How to make bread without yeast?
Flour and water, leave it on counter
Yeast and bacteria from the air
44
Phylum
Next after domain
Environmental analysis suggests greater than 80 phyla bacteria
Therefore huge amount of diversity
45
Proteobacteria
Largest phyla in bacteria domain
Well characterized species
Metabolically diverse
Gr - cell wall
Disease causing
46
What criteria needed for differentiation of bacteria phyla?
Cell wall composition
Genetics
Habitat
Metabolism
Etc…
47
Rickettsia
Spread by incests
Causes Rocky Mountain spotted fever
Replicates in host cell nucleus
Intracellular parasite
48
What causes what looks like tree knots?
Bacterial infection
Tumors in the trees are caused by agro bacterium tumefaciens
49
Agro bacterium tumefaciens
Infects plants
Causes tumors
Infects galls
Has Ti plasmid which is required to cause these infections
DNA is transferred from bacterium to plant
50
How is the Ti plasmid useful?
Has been notified by researchers so plant species become GMOs
Take out tumor DNA and put in desirable DNA
Creates notified crops
51
Enteric bacteria
Facultative anaerobes
Oxidase negative
Catalase positive
Different phyla have bacteria with gr + cell walls
52
Bacillus thuringiensis (Bt)
Is pathogenic to incests
Produces toxin that kills incests
Toxin is called Bt
53
Bt corn
Transgenic corn that produces toxin to kill incests therefore corn is an insecticide
54
Negatives of Bt corn
Bt gene can be transferred to other plants
Could kill harmless incests
Ecological impact is not very well understood
55
Actinomyces
Filamentous bacilli
Common in soils
56
Streptomyces
Another soil bacterium
Produces antibiotics
Synthesis requires large # of genes
Very large genomes > 8 mbp
57
Bactroides
Intestinal tract
Obligate anaerobes are present in significant numbers
Large number of genes - carbohydrate metabolism
58
Chlamydia
Obligate intracellular parasites
Life cycle - 2 forms:
Elementary body: resistant to dry, is used for dispersal
Reticulate body: vegetative form. Divided by binary fission
59
Bacterial species
Depends on genetics
Membranes of a species:
genetically and phenotypically cohesive, monophylogenetic
Should share common recent ancestor to the exclusion of other species
Pan genome has lots because of horizontal gene transfer
60
Traits most important
genome/genomic similarity
61
DNA hybridization
label DNA from one species:
shear it into small pieces
heat it to denature DNA
Second isolate (species/strain):
Denature and shear the DNA
Mix denatured DNA from species 1 and 2
Allow it to cool do DNA strands reanneal
Calculate the percent of the probe hybridized to a control
62
What do the DNA hybridization values mean?
If the hybridization value is less than 70% then they are separate species
Greater than 70% = same species
63
Analysis for DNA sequences to figure out if they are related
Analysis of 16S (ribosomal RNA gene) sequences
Same species have 97% identical species
64
Core genome
Shared by all organisms within the same species
65
Pan genome
is much larger
Total gene #'s and all strains
So large from horizontal gene transfer
Allows for the acquiring of new genes. Also constant deletion of genes from genome as well if the genes aren't being used
66
Why do core genomes not get lost?
Not core since those are proteins with key functions
Most would be essential
67
What organism do we know the most about?
E. Coli
68
E. Coli k-12
Common lab strain
~4.6mpb in size and 4,288 genes
One of the first genome to be sequenced
69
How identical are E. coli K-12 to E. coli 0157:H7
Same species but genetic variation, horizontal gene transfer
70
E. coli 0157:H7
Can infect hamburger
71
Best way to characterize microbial community?
Do rRNA gene analysis
72
Species richness
total number of different species
73
microbial population
group of microorganism of the same species that reside in the same place at the same time
74
microbial community
populations of microbial species coexisting in a specific area at the same time
75
species abdundance
proportion of each species in a community
76
factors that impact species richness/abundance
nutrients
conditions (O2, temp.)
can also change rapidly
77
guilds
microbial populations that exploit the same resources in similar ways
78
Communities of microbes
photic zone: oxygenic phototrophs
oxic zone: aerobes and facultative aerobes
anoxic sediments
79
Niche
habitat shared by a guild that supplies resources, conditions, that cells require to grow
80
Biogeochemical cycling
C, N, S, Fe
Resources may be intermittently available
Feast/famine situation for microbes in environment
Some microbes use storage polymers when nutrients are limiting
Phosphates ---> polyphosphates
81
Competition for nutrients
Can be intense
Polyphosphates and sulfur stored in some cells because of this
82
syntrophy
When microbial species work together to carry out transformation that they could not accomplish individually
83
Complementary metabolisms
Between different species
One species provides something the other is lacking
ej. ammonia oxidizing microbe reduces nitrate and nitrite. Nitrites are substrates for nitrite oxidizing microbes. Therefore they are often found together
84
Study of microbes uses:
Culture independent techniques
Culture-dependent techniques
Isolate ~1% of all microbes present
85
Requirements for microbial growth
Some cases it is unknown
May be dependent on other microbes for growth (big issue in terms of not being able to isolate all the species
86
Culture independent analysis
Most common way is to isolate DNA from a sample. Want to make sure method for isolating DNA would lyse all cells to get all DNA
Kits available to get bacteria from soil, water, and other sample sites
87
Pace approach
Use PCR to amplify the 16S ribosomal RNA gene
88
Why are 16S RNA used in studies?
Conserved with conserved functions
Part of core genome
Core candidate for horizontal gene transfer with organisms have copies of them
Can be targets for PCR primers
Gene is long and there are variable regions meaning you can create a phylogenetic tree to look at evolutionary relationships and identify species based on their unique 16S sequences
89
What can you do with 16S PCR product?
Can clone the PCR products into plasmids with goal each plasmid contains a single one 16S gene insert
90
Challenges of cloning 16S PCR products?
DNA isolation: Substances in soil (contaminants) can inhibit PCR
One eyed king article: how universal are the primers? Could still have organisms not identified because of this approach
91
Better way of cloning 16S PCR products?
Primers to bacteria, primers to archaea and primers to eukaryote
Total diversity can be figured out using all of these primers
92
Environmental shot-gun sequencing?
Applied technique to microbial population
Isolating huge amounts if DNA from environment
Sequence- ended up with million base pairs of non-redundant DNA sequences
18,000 genomic species, 148 previously unknown bacterial phylotypes
Bret force, $$
93
How do antibiotics work?
target bacterial cell wall and ribosomes
94
When was penicillin discovered?
Late 1920s by Alexander Fleming
Went on vacation, left culture on bench in his lab
Mold growing on one of the plates with a zone of inhibition on the plate
Mold produced a substance that inhibited bacteria growth
Penicillin inhibited growth of staph and other bacteria. Did not work on Tb and the flu
If he tried it would have worked on syphilis
95
Floney
Injected 8 mice with lethal dose of streptococcus
4 mice- penicillin --> mice lived
4 mice- no treatment --> mice died
96
Lederberg 1957
Grew bacteria in the prescence of penicillin
Prevents the growth
If he switched bacteria to hypertonic (high salt) media the bacteria grew/survived
Therefore cell does not die due to osmotic lysis and survives. The cells that died had a compromised cell wall from the penicillin
97
What does penicillin do to bacteria cells?
It blocks last step in synthesis of peptidoglycan
Prevents crosslinking between NAG strands
Inactivates enzyme 9transpeptidase) which causes crosslinks
Therefore it is most effective against gram + bacteria
98
Antibiotic targets
Structures absent in eukaryotes or structures that have different structure than eukaryotes
99
Waksman Nobel prize of 1952
Discovered streptomycin in 1944 which is effective against Tb and gr - and gr + bacteria
Targets bacterial ribosome (which kills cells because then they cannot make proteins)
100
Where are antibiotics in nature
microbes in the soil
want to prevent growth of other microbes to have a competitive advantage
This causes organisms to get resistance
101
How microbes get resistance to antibiotics
coded by a gene which can cleave antibiotics to make them ineffective
Genes can be transferred to other microbes via HGT
102
Best way to treat C. Diff infection
Fecal transplant surgery
More effective than antibiotics
103
Different mechanisms for antibiotic resistant
1. Prevent it from entering the cell
-Decreased uptake and or pump the antibiotic out of the cell
2. Target modification
-Mutation in gene that makes target. Changes structure enough to not be identified
3. Enzymatic degradation
-Degradation of the antibiotic which inactivates it
4. Bypass pathway
-Folic acid biosynthesis or nucleic acid synthesis or altering target site. Over production of target
104
Where are most antibiotics used in the U.S.?
On farms on healthy animals
105
Potential impact of using antibiotics on farms?
Superbugs from selective pressure and antibiotic resistant strains
106
How do we overcome antibiotic resistance?
Modify existing antibiotics to develop/discover new antibiotics
107
Is it possible for a bacterium to survive antibiotics if they do not possess or acquire (through horizontal gene transfer or spontaneous mutation) resistance?
Yes, with persistence
108
Persistance
Cells that are susceptible to antibiotics and are not affected because they are dormant
Examples: Tb and pseudomonas
109
Toxin-antitoxin (TA) molecules
Bacteria have TA loci
Is one gene that makes a toxin that inhibits the growth of bacteria
Another gene is the antitoxin and counters the activity of the toxin. Bacteria will have slow growth and persistence
Therefore they work in synergy
110
HipAB complex in E.Coli
Have 30 toxin and antitoxin modules
hipA makes toxin that inhibits translation
bipB encodes the antitoxin
hipB protein is susceptible to a protease
111
In hipAB complex what happens if hipA is not present?
cell grows because of translation
112
hipAB complex in times of stress
Protease is active and will cleave hipB, hipA is free and inhibits translation
Bacteria becomes dormant and binds to promoter region to increase transcription (Ask him about this not very sure here)
113
iChip
Isolates bacteria from soil
Contains chambers and semipermeable membranes
membranes allow for diffusion of nutrients
using technique, gotten 50% recovery of microbes compared to the 1% using traditional petri dish techniques
114
iChip steps
1. Soil is diluted to have 1cell/chamber
2. Cover the iChip and put it in soil so organisms will grow
3. Took extracts from 10,000 isolates of organisms. Looked for antimicrobial activity against S. aureus
4. From 10,000 isolates, found new species that is effective against S. aureus
5. Sequences genomes of species and then isolated the antimicrobial compound
6. Used mass spec and NMR to determine the structure of the compound
7. Gave compound a name: Teixobactin which is a new antibiotic
8. Identified new genes that encode proteins to synthesize Teixobactin
115
Teixobactin's effectiveness
Is great antimicrobial activity against Gr + pathogens and microbacterium
