Midterm 1 Flashcards
How long ago did Bacteria and Archaea diverge?
~2 billion years ago
Deinococcus radiodurans
most radiation resistant organism ever known.
Conum the bacterium. Can survive 1000x the dose that would kill humans.
It has multiple copies of its genome that can be used as a backup after being exposed to the high radiation. It will then repair the previously exposed genome
Robert Hooke
First one to describe microbes. Illustrated the fruiting structure of molds
Antoni van Leeuwenhoek
He is considered the FIRST microbiologist. First one to describe bacteria (microscopes were more advanced at this time).
Louis Pasteur
Discovered fermentation and that alcohol fermentation was a biologically (as well as chemically) mediated process.
Disproved theory of spontaneous generation
Led to the development of methods for controlling the growth of microorganisms (aseptic technique)
Robert Koch
Demonstrated the link between microbes and infectious diseases.
Identified the causative agents for anthrax and tuberculosis
developed techniques (solid agar + Walter Hesse) for obtaining pure cultures of microbes.
Koch’s postulates
For proving cause and effect in infectious diseases
1. susp pathogen must be present in all cases
2. susp pathogen must be grown in culture
3. these cells must then cause associated disease upon introduction to healthy idvl
4. the susp pathogen must be isolated and show to be the same as the originall
Sergei Winogradsky
Demonstrated that specific bacteria are linked to specific biogeochemical transformations.
Proposed the concept of chemolithotrophy (oxidation of inorganic compounds to yield energy)
Demonstrated that chemolithotrophs are often autotrophs (ie they obtain carbon from carbon dioxide)
nitrogen fixation (N2 - NH3) and nitrification (NH3 - NO3-)
what is the winogradsky column?
Mixed water and dirt - eventually get a column with different colours and bacteria in each row of the column carrying out different chemical reactions (associated with their metabolism). No oxygen at bottom - where the sulfate oxidizing bacteria thrive
Ferdinand Cohn
Father of bacterial taxonomy. First to classify different species of bacteria.
He coined the term bacteria (small rod or staff)
Different cell shapes (look for images)
filamentous
spirillum
spirochete
budding and appendaged
What is a lithotroph?
energy source is inorganic chemicals
What is a phototroph?
Energy source is light
What is an organotroph?
Energy source is organic carbon
What is an autotroph?
carbon source is carbon dioxide
what is a heterotroph?
carbon source is organ carbon
What is a chemotroph?
Get their energy from chemicals
Energy source
Litho vs photo vs organo
Carbon source
Hetero vs auto
WHAT IS the largest pool of carbon on earth?
CO2 in the atmosphere
what is genetics vs genomics
Genomics - the studying of the entire genome
Genetics - just studying a few genes, but not all genes in the genome.
What is the ANI?
average nucleotide identity. It is an in silico methodof comparing two genomes computationally (basically tells us
What does Haeckel’s tree look like?
It is based on the belief that evolution strives towards increased complexity
But he was the first to recognize that microbes are quite important.
Moneres (@ bottom incl. bacteria)
Carl Woese
Decided that we should stop drawing the tree of life based on thought experiments or on fuzzy data like morphology but instead we should draw it based on hard, quantitative data like DNA.
- identified the rRNA gene as a good gene to track because it needed to be a gene that every organism on earth had, needed to be universal, and needed to mutate slowly and at a constant rate (so the mutations would act like a biological clock in a sense).
EVERY LIFE FORM THAT WE KNOW HAS RIBOSOMES
SSU rRNA or 16s rRNA
named Archaea
3 domain system - puts everyone in their place in terms of evolutionary ideas (not towards increased complexity).
How are phylogenetic trees constructed?
Taxonomic classification based on evolutionary history.
Align homologous sequences and compare. Find regions of homology and then start counting the differences
what are the four phyla of Bacteria?
Proteobacteria*
Actinobacteria
Firmicutes
Bacteroidetes
What are candidate phyla?
Groups of bacteria that actually have not been characterized/grown in the lab. They are just defined by environmental sequences.
Proteobacteria
40% of all cultured bacteria sp are Proteobacteria
Bacteria phylum
The most abundant and diverse group in nature. Divided into classes based on greek alphabet letters.
Endosymbiotic theory of eukaryotes
Mitochondria and chloroplasts are descendants of respiratory and bacterial cells respectively.
Absorbed by ancient-archaeal-like cells but instead of being destroyed, formed a mutual relationship
Supported by the fact that:
-Eukaryote have T and translational machinery most similar to those of Archaea
-Chloro and Mito are about the same size as bacterial cells and they independently replicate from the rest of the cell
-Mito and Chloro contain their own circular genomes that contain 16s rRNA (most-convincing evidence)
polyphasic approach
A method used to describe bacterial species. This requires a description of:
- Morphology (incl. chemical composition, Gram reaction, lipid composition, etc)
- Metabolism (energy and carbon source)
- genotype (DNA hybridization DDH or average nucleotide identity ANI to compare the genomes of related species (most important factor)
- phylogeny
If organisms have greater than 97% shared 16s rRNA similarity, are they the same species?
Not necessarily. They can be diff sp if their genomes are quite diff (often due to a strong selective pressure + rapid mutation rate of the genome)
Same species when?
Both the 16s rRNA sequence similarity is above 97% and when the ANI is above 96 or so.
What does 16s rRNA sequence similarity tell us?
The less similar the sequences, the longer ago that the species diverged.
Also if the similarity is lower than 97%, the two organisms being compared are not categorized as being the same species.
What does the ANI tell us when classifying species?
The lower the ANI, the more confident that we can be that they are different species.
What does the formal validation of a new prokaryotic species require?
Detailed description of the characteristics/features (metab, genetic comparisons, metab)
deposition of viable cultures of the organism in at least two international collections
proposal of a latin name and a publication in the International Journal of Systematic and Evolutionary Microbiology
Classification of the prokaryotic grouping hierarchy
Dinos -Domain
Playing - Phyla
Cards - Class
On - Order
Fine - Family
Greek - genus
Silk - species
species richness
Total number of species present in a given area
species abundance
the population size of each species in an ecosystem
Guilds
Metabolically-related microbial populations (perform similar metabolic rxns)
Perform key steps in biogeochemical cycles
rhizosphere
the area around plant roots where plants secrete sugars and other compounds
-rich in organic matter and microbial life
What are the most diverse habitats for microbes?
The soil
What is an OTU?
Operational taxonomic unit - usually defined as a 16s rRNA sequence that differs from all other sequences by >3%.
So OTU’s are presumed to represent a species
so this underestimates the amount of species… because there are some bacteria who have similar 16s rRNA sequences but different enough genomes to be classified as different species.
Proteus
Shape-shifter
syntrophy
when 2 organisms can breakdown a substance that neither one can degrade alone
one organism feeding on the metabolic products of another
Prochlorococcus
responsible for greater than 40% of the marine phototrophs
responsible for about 50% of the net productivity of the ocean
Pelagibacter
The most abundant marine organoheterotroph. It is an oligotroph that has not been validated as a true species
Contains proteorhodopsin - allows cells to use light energy to drive ATP synthesis.
-not considered a phototroph
Which phyla of bacteria are most abundant in the human microbiome?
Bacteroidetes and Firmicutes (Proteobacteria are not as relevant here)
quorum sensing
sensing and responding to the population density is critical in the development and maintenance of a biofilm.
Major quorum sensing molecules are: acetylated homoserine lactones
For which medical treatments are biofilms a large problem for?
Medical implants like catheters and artificial joints
extra - biofilms have been implicated in several medical and dental conditions like periodontal disease, kidney stones, tuberculosis, legionnaires’ disease, and Staphylococcus infections.
microbial mats
Very thick biofilm formations
stromalites
Microbial mats made of phototrophic bacteria.
Have existed for over 4.5 billion years
Mesophile
Loves mild temperatures. 5-45 degree celsius
Thermophile
45-80
Psychrophile
less than 15 degrees
Which do better at really hot temperatures, Bacteria or Archaea?
Archaea.
No eukaryotes can live above 62 degrees celsius (ie. there is no hyperthermophilic eukaryotic organism)
Methanpyrus kandlerii grows at 122 degrees celsius - hyperthermal vents
wHAT metabolic features do almost all hyperthermophiles exhibit?
Hydrogen or sulfur oxidation (extract energy from inorganic chemicals)
Are there phototrophic hyperthermophiles?
No. Photosynthesis stops at 73 degrees
What adaptations do microbes have to function in hot environments?
- have stronger bonds to stabilize proteins
- increase RNA and DNA stability (GC content, reverse gyrase)
- decrease membrane fluidity
- thermophilic enzymes and proteins function optimally at higher temperatures
Features of enzymes that provide thermal stability?
-Amino acid substitutions in a few locations that provide more heat - resistant folds
- increase number of ionic bonds (salt bridges are strong)
-highly hydrophobic interior
-production of solutes that help stabilize proteins
- smaller more spherical proteins with less 4 structure
TAQ POLYMERASE - heat resistant enzyme for DNA replication in thermophiles
- thermus aquaticus
What does reverse gyrase do?
Positively supercoils DNA prevent melting/denaturation
What does RNA do to prevent melting at higher Ts?
higher GC content
acidophile membranes
has a proton pump to pump out protons. Protons come in via to F0F11 ATPase to generate ATP
Alkaliphiles
Have a proton pump to pump protons INTO the cell vs out
No proton motive force, F0F1 ATPase isnt used.
Na+ is pumped out of the cell and comes in through a Na+ type F0F1 ATPase to generate ATP.
Have an Na+/H+ antiporter that pumps Na+ out and H+ in.
Halophiles
Like environments with low water activity due to SALT
also an osmophile (low WA in general)
like 1-15% of NaCl in salt
Sea water - 3.5% – typically grow best here
Hypersaline means that something has more salt in it than sea water.
Xerophiles
Low water activity due to another reason besides high salt presence
also an osmophile (low WA in general)
What is the % of salt in water for it to be fully saturated?
35.8%
what does having a low water activity mean?
It means having relatively more solutes in it
lower pressure when there are more solutes
water moves from regions of high water activity to low activity
Plasmolysis
shriveling
occurs when water leaves the cell
water moved from high to low WA
What is the salt in strategy?
Halophile strategy - mostly Archaea do this!
accumulate KCl (need salt-adapted enzymes for this)
Have transporters to pump in salt
Cheaper strategy
Compatible solutes strategy
Halophile strategy - Bacteria and Archaea use this strategy
Accumulate non-charged organic solutes (don’t damage enzymes like salts do)
This strategy is more expensive
What is the minimum water activity required for growth of halophiles?
0.75
This is relatively quite low!
solutes: ectoine, trehalose, glycine betaine
Have a chemosensitive channelo that opens with increase in pressure - releases solutes quickly if its exposed to fresh water.
What percentage of the atmosphere is oxygen?
21% oxygen
Aerobes
require O2 for respiration
Microaerophiles
require O2 but at less than atmospheric levels. They have some enzymes that are damaged by oxygen but they require it for respiration
Facultative anaerobes
Can respire O2 but they do not require it.
They will often choose to respire O2 if it is available as this generates more energy.
Aerotolerant anaerobes
They DO NOT respire O2 but they are not damaged by oxygen
obligate anaerobes
They do not respire O2 and THEY ARE damaged by it
evolved before the atmosphere had oxygen
Which organisms can respire O2?
facultative anaerobes.
microaerophiles
aerobes
Which organisms do not respire O2?
aerotolerant anaerobes
obligate anaerobes.
What is a thioglycate broth?
Complex medium that separates microbes based on oxygen requirements
Reacts with oxygen so oxygen can only penetrate a few mm from the top.
Reactive oxygen species include:
Super oxide anion (O2-), hydrogen peroxide H2O2 and hydroxyl radical
These are made by accident and they are stronger oxidants O2 itself
catalase
enzyme that destroys ROS
hydrogen peroxide –> water and O2
peroxidase
enzyme that destroys ROS
hydrogen peroxide and H –> water NAD
superoxide dismutase
enzyme that destroys ROS
O2- and O2- and H+ –> H202
also need catalase or peroxidase
Enzymes that get rid of H202`
catalase and peroxidase
superoxide reductase
O2- and H+ and rubredoxin –> H202
also need catalase or peroxidas
Gram Positive
have a very thick wall of peptidoglycan
Stains purple
Firmicutes, Actinobacteria, some Chloriflexi
cross link often contains peptide interbridges
cell wall contains teichoic acids (none in Gram-)
Gram negative
most bacteria
Have a thin wall of PG
have a cytoplasmic and an outer cell membrane
Stains pink
cross links between DAP and the D-alanine carboxyl on an adjacent strand
single layer of PG
Lipid layer in bacterial cytoplasmic membrane
- 2 ester linkages that connect the fatty acids to the glycerol (diester linkage)
- usually the FA tails are quite saturated (more unsaturated in cooler conditions - adaptation)
thermophiles - mostly all single bonds
psychrophiles - have some more double bonds
archaeal membranes
they have ether linkages connecting the tails to the head groups
lack fatty acids but instead have isoprene units
can have bilayers with diethers or monolayers with tetraethers. or a mixture of both.
what makes archaea better withstand heat than bacteria?
ether linkages are more thermostable
ability to form monolayers in their membrane - makes the membrane less fluid
What are the 3 components of the ABC system?
Active transport mechanism
(periplasmic) Binding protein, transmembrane transporter, ATP-hydrolyzing protein.
group translocation
series of proteins, chemical modification, high E phosphate.
active transport mechanism
What is the periplasm?
The space between the inner and outer membrane in Gram negative bacteria.
What are cell envelopes made out of?
cell membranes, cell walls, S layers (not always present)
In Gram negative bacteria, we consider the outer cell membrane to be part of the cell wall.
Gram stain process
Crystal violet (stain) - iodine (assist CV complex to the cell wall) - alcohol (decolourant) - safarin (counterstain)
which domains have peptidoglycan?
Only bacteria, Archaea and Eukarya do not have PG
What is glycan tetrapeptide made of?
sugar backbone with alternating N-acetylglucosamine and N-acetylmuramic acid joined by B-1,4 linkages
- short peptide attached to N-acetylmuramic acid
- alanine, glutamic acid, lysine, diaminopimelic acid DAP
diaminopimelic acid DAP
has sites for peptide cross-link formation and is only found in peptidoglycan– adapted for this purpose.
teichoic acids
These are only present in the cell wall of some Gram + bacteria.
Good for targeting unwanted Gram +bacteria in the body.
acidic and negatively charged
strongly antigenic
covalently bound to PG
Functions:
maintain the porosity of the cell wall
anchor the cell wall to the membrane
help maintain cell shape
capture essential ions
can be a reservoir of phosphate
regulate cell wall turnover
Has autolysins (lysins that lyse the own cell) - break down old cell wall in order to build more.
lipopolysaccharides
extending out from the outer membrane in Gram - bacteria.
- facilitates surface recognition, important virulence factors, and add strength
- good for creating biofilms
- these are only found in bacteria so they are good targets for targeting bacterial diseases.
Structure: Lipid A - Core polysaccharide - repeating polysaccharide.
Lipid A
fatty acid tail and glycerol/glucose that forms part of lipopolysaccharides
This part of the bacterium can often cause damage to humans (or others) with bacterial diseases. It is an endotoxin and can cause endotoxic shock.
