Quiz#1-Bacteria and Archaea Flashcards
rRNA
This is the type of RNA that is contained in ribosomes(molecular factory
Ribosomes
complexes of RNA found in both prokaryotes and Eukaryotes. Their function is to synthesize proteins by nucleic acids are coded and linked to Amino Acids to make proteins.
Organelles
Membrane compartments in eukaryotes, that are specialized in a specific function, defined by the reactions they can carry out.
Nucleoid
Region in a prokayotic cell that contains the DNA
Peptidoglycan
A polymer of amino acids sugars crosslinked to peptides, it serves as a layer around the cell and is enclosed by and outer membrane.
flagella
long, whip-like attachment of a prokaryote that propells the cell allowing it to swim
Domain
a subjective term used for the largest groups of life
Pilus
hailrlike structures attached to the surface of some bacteria, serving to stick to other bacteria and exchange genetic material.
rRNA has been incredibly important for phylogenetic analysis of microbes(for that matter all life). Why?
B/C phylogeny is based on the differences in the sequences of nucleotides in the cells rRNA, the comparison using rRNA is also useful b/c qll rRNA molecules have the same function and they have a structure that changes very little overtime, therefore comparison becomes easy and helpful in phylogeny.
What are biofilms and their importance
biofilms are microbial communities that uses matrices of polycharides to trap other cells and make layers. the importance is that this will make it more difficult to treat pathogenic bacteria since this layer may be impermeable and will resist the antibiotics.
What are the differences btw a prokaryote and a eukaryote?
in prokaryotes the difference is that there is no nucleus nor compartments of organelles that specialize in diff functions,,,,also the cells are much smaller than eukaryotes, and reproduce through binary fission rather then meiosis or mitosis(eukaryotes)…
what is the difference btw aerobic and anaerobic?
anaerobic conditions is in the absence of oxygen while aerobic is requiring oxygen to proceed with metabolic processes.
Binary fission
the reproduction of prokaryotic cells in which the cell divides into two comparable(similar)
gram stain
a staining test that separates or distinguishes between gram positive(when stained appear blue to purple) and gram negative(turns from pink to red)
transformation
gene transfer from the environment to a bacteria
lateral gene transfer(can lead to discordant gene trees
transfer of genes(plasmids)from one species to another, moving sideways,,it may even be among extremely distantly related forms….through this genevtranfer of plasmids bacteria is able to exchange resistance to antibiotics…this is why mire attention is given to prescribing antibiotics….itd debateable whether it may complicate phylogeny analysis since now you can reference entire genomes uncomplicated by LGT
plasmid
small molecules of replicating, circular, extra-chromosomal DNA found in bacteria. It is able to transfer genetically
asexual reproduction
reproduction without mating
chemoheterotroph
(all three domains)obtains carbon and energy from organic compounds
chemolithotroph
some bacteria and archaea)obtains carbon via CO2 and energy from oxidizing inorganic compounds…also called chemoautotroph
anaerobe
in the absence of oxygen b/c it may be poisonous as it was in the beginning of prokaryotic life.an anaerobe therefore does not use oxygen as an electron acceptor in metabolic process like cellular respiration(energy formation process)
aerobe
in the presence of oxygen or requiring oxygen to undergo cellular respiration and therefore to survive.
what are the characteristics of prokaryotic cell walls?
(made up of the peptidoglycan and outer membrane)…..most prokaryotes have a cell wall outside the cell plasma membrane, and the rigidity of the cell wall supports the structure and determines its shape. Most bacteria contain peptidoglycan whcih forms a single giant molecule around the entire cell, which is then enclosed by an outermembrane in some bacteria. Some also contain a capsule surrounding the cell wall
biofilm
microorganisms embedded in a polysaccharide matrix forming a resistant coating on moist surfaces
bacteria
are prokaryotic cells that have same structure components of eukaryotes. Contain cell walls with peptidoglycan, both Gram-positive and gram-negative…can be shaped like a rod spherical and helical forms
eukarya
the domain of life containing unbranched fatty acid with glycerol and an ester linkage. Not all of them contain a cell wall but those that do have one dont have peptidoglycan. Also have unique rRNA.kingdoms of protists, plants, fungi, and animals.
archaea
is one of the three domains of life, they are prokaryotes that have membrane made of branched hydrocarbon chains,with glycerol and an ether linkage, The archaea contain no peptidoglycan and have unique rRNA than the other tow domains. They live in extreme environments(halophile–salty, hyperthermophiles, and methanogens) thanks to their ether linkage,
phylotyping
classification of groups or taxa depending on determining the rRNA sequence(in all organisms)… And comparing this within the sample..this can lead to building evolutionary trees by identifying orgsnisms based on the position of small subunit(ss) rRNA genes…the disadvntge is that it can help group but not identify what for ex a sample of orgnsms does..(thats when genomes become essential)
conjugation
two bacterium involved)the transfer of genes from a donor to receptor bacterium,,,btw male and female…the recipient is the one lacking the f factor or extra DNA piece…
transduction
transfer of genes via a bacteriophage that carries the piece of DNA and injects it onto a bacterium therefore adding it to the bacteria’s DNA
What is the primary way that prokaryotes reporduce?
binary fission which is an asexual reproduction where cells divide into two similar cells. most prokaryotes have a single chromosome-a long DNA molecule with proteins bound to it. circular
chromosomes are characteristics of prokaryotes…the DNA molecules have an ori(origin of replication) and a ter(where replication ends)…as replication proceeds the ori moves toward the opposite end of the cell..After the replication is complete the cells divide via cytokinesis
What is the lateral gene transfer(LGT)? what are the primary mechanisms of LGT in prokaryotes?
transfer of prokaryotic genes from one species to the other….”sideways”…this can occur through transformation, and transfer by plasmids and viruses
Photoheterotroph
(some bacteria)use light as energy source but carbon from organic compounds that other organisms produce…example compounds released by plant roots
photoautotroph
(all three domians)organisms that obtain energy through photosynthesis, using light source for energy and CO2 for their carbon source
nitrogen fixation
nitrogen is required by all organisms to build proteins, nucleic acids and other compounds. therefore nitrogen fixation is vital, carried out by a variety or archaea and bacteria, but no other organisms….it occurs by the formation of ammonia from atmospheric n2
eukaryote
cells that are believed to have derived from endosymbiosis(ingesting smaller prokaryotes). they are more specialized cells due to the compartments(organelles) that they have
What are the major ways that prokaryotes(and all organisms for that matter) obtain their energy, carbon, and nitrogen?
chemolithotroph, photoautotroph, chemheterolithotroph,photoheterotroph, photoatotroph….explain….and denitrifiers are bacteria that release n2, and use no3 nitrate as an electron acceptor in anaerobic conditions….nitrogen fixation occurs in archaea and bacteria only,thus we are extremely dependent on them
Prokaryote
organisms found in the two domains of archaea and bacteria, doesn’t have membrane-enclosed compartments.no nucleus but are said to be the first cells evolved
Genetic recombination
Occurs in bith bith bacteria and archaea but not as a part of reproduction
what are the differences btw archaea and bacteria?
while not much is known about archaea they can tolerate very harsh environments, such as salty acidic, or extreme temperatures…they have different structures than bacteria bc they dont have peptidoglycans and instead of ester linkage they have ether linkage to branched hydrocarboons and glycerol…they both do have unique rRNA…these two domains are highly divergent from each other and distantly related on the tree of life…..yet both are single celled prokaryotic cells that contain DNA, RNA, and synthesize proteins via transcription and translation
alignment
is used in phylogenomics when trying to identify an organisms gene functions,,,you obtain a homolog sequence, then align the sequences and then make a phylogram showing the dna evolution, but instead of choosing the function of the gene to be the one with highest gene similarity,,,its the one with the most likely or parsimonious gene function.
vertical transmission
occurs to pass down genes form parentto daughter cells, whcih is how it usually ocuurs so there is a transfer of genes vertically between related lineages
disease
continuous irritations expressed through symptoms…can be due to the interactions(-..+) interactions btw organisms.
cyanobacteria
is the bacteria-prokaryote that was engulfed through an endosymbiosis event to create the eukaryote with a chloroplast organelle
proteobacteria
the prokaryote involved in primary endoysimbiosis where a eukaryotic cell engulfed it and it then evolved into the mitochondria organelle
firmicute
gram + bacteria
mutualsim
symbioisis btw tow organisms that results in a +, +intereaction where both organisms benefit….
commensalism
interaction btw organisms where one benefits and other is not affected
parasitism
interaction where one benefits and the other is affected..+, - interaction..may or may not be a pathogenic
pathgen
bio agent that causes disease
thermophilic
there can be archaea and bacteria extremophiles, where in this case they can resisist very high temperatures, in fact sometimes their optimal temperatures are extremely high ..thermophily is sure to have evolved convergently
exteremophiles
bacteria or archaea resisting conditions that in our context are dfficult to survive in it..
halophile
organisms that is ale to survive in very salty environments
metagenomics
function of genes other that ribosomal genes to determine whether one is turned off or on
haplontic
some protists exhibit both asexual and sexual life cycles,,,and so a haplontic is one where the dominant phase is the haploid stage and only the zygote is diploid..because then it undergoes meiosis to produce spore that are again haploid…which go on to produce the new gametophyte after
diplontic
is another life cycle(alt of gen) that protists undergo where the gametes are the only haploid stages and the rest is diploid.
plasmodial slime molds
individual motile cells that are followed by formation of single multi-nucleate cell(eg..plasmodium)…so they eat bacteria as they go until making a joint organization where they gather multiple organism to create back and forth flowing movement.
cellular slime molds
similar to plasmodial… but each of the unifying cells maintains its individuality …so its the aggregation of individual cells to a single place in order to repoduce across a substrate..it can make fruiting bodies
aplicomplexes
microbial protists thtat are in all parasites of animalls and have complex life cycles involving two hosts…ex is in the disease malaria(both in mosquito and human red blood cells)
quroem sensing
intra and inter cellular communication between bacteria, where it can distinguish btw self and other..where each make signals that are sensed by receptors, until the number of signals is enough to indicate there are enough bacteria to carry out a task..important to understand b/c if we can stop this communication we can find ways pf treating diseases
zoonotic disease
disease form animal to human or human to animal…ex..plagues occurring btw rats..and animal..influenza…there’s five stages…first animal to animal…2)animal to human but not to much to wear it spreads btw humans 3) animal to human and then to other humans..but not too serious..4) then its animal to human to human and it becomes a disease outbreak..5) the disease because exclusively human…such as HIV
gram stain
helps determine what type of bacteria it is …if positive or negative…which is important to prescribing antibiotics…since it may e know that if its positive than it will change from pink to purple..and if negative..from pink to red..and identify if it has a thick or think peptidoglycan layer..and efficiently treat…
Archea–two main clades
crenarchaeota and euryarchaeota…the fist is a thermophilic and acidophilic while the later are methanogens releasing 2 billion tons/year
biofilm importance
associated with infectious bacteria(involved in the quorem communication), dental plaque, corrosion in pipes….but positive aspects are that they are important to protect ourselves against pathogens,
methanogen
only found in archaea clade…they produce about 2 billion tons a year…Archea in the guts of animals and so then from their waste it enteres the atmosphere…its also in hydro-thermal vents
protist
eukaryotes that are not plants animals or fungi are places in this paraphyletic group …they can be symbiotic, pa
thogenic, but alsso source of petroleum and natural gas
nitrogen fixation
microbes importatn in this..both aarchaea and bacteria can fix nitrogen and allow for nutrirent uptake and the thermophile used to make enzymes–novoenzymes
envelope
is the lipid membrane in virusees that alon with proetein coat are among the two key fts of a virus
