microbes Flashcards
midterm 1
what is the tree of life?
- refers to descendant-ancestor connections across all living things
- represents the common ancestry of all life
- the simile of tree came from Darwin
What is meant by universal homology?
- characters found in all living things
- all life is related therefor some features will be the same due to common ancestor
provide examples of universal homology
DNA and RNA and Lipoprotein Cell Membrane
Ribosome
Mitochondria is not UH
Ribosomes
RNA is translated into protein using ribosomes
Ribosome’s structure and function is conserved throughout life
DNA to RNA
DNA (ACTG) -> transcription -> RNA (ACUG)
history of three domains tree
carl woose examined the rRNA (ribosomes) and divided it from bacteria, archaea bacteria, and eukaryotes
-Arcahe nd eukarya are sister taxa
history:
- Aristotle had the great chain of being, where it suggested that all organisms tries to climb the great chain of being, which ultimately leads up to God
- Charles Darwin proposed that all organisms had a single common ancestor
- Ernst Hackel divided organisms into 3 kingdoms: plantate, protista, animalia
- Whittaker: 5 kingdom tree - plantae, fungi, animalia, protista, monera
prokaryote
Archaea and bacteria are prokaryotes
they lack a nucleus
pro= before
karyon = nucleus
two domain vs three domain tree of life
in three domain archaea and eukarya are sisters… in two domain eukaryotes is only sisters to SOME of archaea
two domain tree (Asgard)
sample study from Loki’s castle = Asgard group of archaea
suggests eukarya is part of archaea
LUCA
Last Universal Common Ancestor
lived near deep sea hypothermal vents
why is microbial morphology and biology problematic for phylogeny reconstruction?
most microbes have the same morphology
many are capable of movemnet
nitrogen fixation
microbes run nitrogen and carbon cycling
virus does not = bacteria
virus does not = bacteria
extremophile
mostly archaea but bacteria and some eukarya are extremophiles as well.
live in extreme environments pH, temperature, and salinity wise
microbiome
“cloud of microbes”
aerobes vs anaerobes
facultative anaerobe
obligate anaerobes
aerotolerant anaerobes
aerobes = needs oxygen anaerobe = does not need oxygen facultative = doesn't need oxygen but will use it when available obligate = oxygen is toxic aerotolerant = can't use oxygen but isn't harmed by it
bacteria and archaea don’t have a chloroplast but.
they can photosynthesize
eukaryote vs. prokaryote (5differences)
Eukaryote ———- Prokaryote
nucleus ------------ no nucleus strand DNA------- circular DNA membrane bound organelles -----none mitosis------binary fusion haploid diploid more ----- haploid
what does mitosis and binary fission result in
aesexual processes that result in identical duplicates
-mutations can occur
eukaryotic cells are able to go through meiosis why can’t prokaryotes?
prokaryotes are haploids
how do bacteria and archaea make new genetic recombinants… (eukaryotes =sex)
lateral gene transfer
lateral gene transfer
- exchange of DNA across lineages (regardless of genetic history)
- vertical transmission of DNA
what are the three mechanisms of LGT in prokaryotes
1) conjugation : bacteria and archaea can directly exchange their genome by transfer of plasmid
2) Transformation : bacteria and archaea pick up chromosomes from environment (usually from dead bacteria or archaea
3) transduction : viruses can transmit DNA from host to host
plasmid
a small circular chromosome not intact with main chromosome… used in conjugation
how is LGT limited
- large/complex sets of genes are less likely to be transferred
- only portions of genome are transferred
how does LGT complicate making of phylogenies
bacteria and archaea can exchange genes even though they are not the same species
-it erases phylogenetic history
can LGT happen in eukaryotes?
Yes ex: snake and cow
if LGT is common how can we reconstruct the phylogeny
1) sample many taxa
2) use multiple genes and compare their results
3) use multiple independent types of data
4) check for congruence or conflict from other trees
the great plate count anomaly
many more cells are present in the environment than can be grown in the lab
What are culture independent DNA studies ?
instead of growing pure lab cultures, go to the environment and sequence environmental sequences
the two types of culture independent DNA studies and the people associated with them
1) pace : DNA
2) Hug et al : genome
peptidoglycan
in cell walls of bacteria
gram positive = thick layer (penicillin will work)
gram negative = thin layer
cross linkages with peptidoglycan make stronger cell walls
how does penicillin work with structure of cell
penecillin will work on gram positive cells (thick layer of peptidoglycan)
multicellularity
bacteria congregate
- division of labor
- some cells give up reproduction
nitrogen fixation
some cyanobacteria are able to fix nitrogen and photosynthesize using folded membranes
biofilms
- communities of organisms that are irreversibly bound to a substrate ; they secrete extracellular polymers (slime)
- a means of way of communicating between prokaryotes that enables them to function multicellularly
quorum sensing
expression of group behavior genes as a result of density dependent interactions
- seen in biofilms
Group Behavior Genes:
- Virulence
- Antibiotics Production
- Sporulation
- Conjugation
cyanobacteria
- photolithoautotrophic
- fix nitrogen
- chloroplast from endosymbiotic cyanobacteria
importance of microbes on human
- digestive microbes
- infant microbe
- psychology
alphaprotobacteria
gram negative bacteria that have common ancestors with mitochondria
gram negative
peptidoglycan in bacteria vs. archaea
peptidoglycan is only present in bacteria not archaea
biofilm key features
Key features:
- Extracellular polysaccharide matrix
- Surface attachment
- solid surface OR
- soft tissues in living organisms - Structural heterogeneity AND diversity (bacteria, archaea, protists, fungi, algae, etc.)
chloroplast and origin
endosymbiotic cyanobacteria
endosymbiosis
explains origin of mitochondria and chloplasts
evidence :
1. mitochondrial/chloroplast size
2. mitochondrial/chloroplast structure and presence of DNA; their DNA is similar in structure, size and shape to bacterial DNA
halophile (extremophile)
live in salty environment
methanogens (extremophile)
produce methane gas as a waste product
thermophiles (extremophile)
live in extreme cold / hot
Gram Stain (q: which cell are antibiotics most likely to be effective?)
Peptidoglycan is sensitive to staining agents. Some antibiotics work by affecting the peptidoglycan layer, and thus cell wall synthesis
- bacteria are characterized by the peptidoglycan layer
- Gram+ bacteria: peptidoglycan layer is thick and outside of the cell wall
- Gram- bacteria: peptidoglycan layer is thing and lies between the plasma membrane and the outer membrane of cell wall
a: antibiotics are most likely to be effective on gram+
**Antibiotics are prescribed to someone by determining if the bacteria is gram+ or gram-
Lateral Gene Transfer
3 different ways & similarities + differences w/ genetic recombination
Similarities:
- both create new genetic combinations
- both may involve recombination
Differences (LGT):
- only involves small part of genome
- not reproduction
- multiple mechanisms
- can occur across large phylogenetic differences
mutualism
symbiosis where both benefit
organelles
An organized or specialized structure within a living cell
gram + vs gram -
A special polymer of amino sugars
- gram+: peptidoglycan is outside of cell wall
- gram-: peptidoglycan is between plasma membrane and outer membrane of cell wall
only bacteria have peptidoglycan
phagocytosis
The ingestion of bacteria or other material by phagocytes and amoeboid protozoans.
photoautotroph
organisms that carryout photsynthesis
photoheterotroph
Organisms that use light for energy, but cannot use carbon dioxide as their sole carbon source
stigmatella
a multicellular organism that is made of many proteobacteria (gram- bacteria)
symbiosis
3 types & why eukaryotes form symbioses
Symbiosis is an association between at least two different organisms in which at least one of them benefits
- Mutualism: both benefit
- Commensalism: one benefits, one does not gain or lose
- Parasitism: one benefits, one suffers
Eukaryotes
- metabolically limited in their capabilities relative to archaea and bacteria
- less able to “acquire” metabolic processes from other species via lateral gene transfer
- eukaryotes can “acquire” more capabilities by engaging in symbiosis with archaea and bacteria
spirochetes
- gram- bacteria
- Motile
- Axial filaments (modified flagella)
- Many are pathogens
stigmatella
a multicellular organism that is made of many proteobacteria (gram- bacteria)
vertical transmission
transmission from parent to child
