Archaeal and Eukaryotic Diversity

what is the main difference between these two groups

their ribosomal RNA sequencing (and sometimes DNA as well)

why are archaea the least studied?

least studied since they are difficult to culture (they prefer to live in the extreme environmnets)

how are some archaea similar to bacteria?

can be unicellular, divide via binary fission (besides differences in how daughter cell remain attached to parent), prokaryotic, around same size, and will grow on standard agar (and to increase admission)

do we use the same shape terminology for archaea?

No

what are two structure unique to archaea? what about a shape that is unique?

structures: cannule and archaellum

shape: square morphology

what are cannule? (do not mention shape)

they are an extracellular structure for cell communication and connection

what is the proposed purpose for cannulae

a passageway for sharing cytoplasmic material but what they are sharing is unknown (ions? proteins? nucleic acid?)

what is the shape of cannulae

hollow tube between two cells

when do cannulae form?

when two daughter cells (connection between the two)

true or false: cannulae remain as archaea die

true but they are not permanent (we do not way)

do archaea follow the central dogma? what is it?

yes dsDNA→ssRNA→protein with the same enzymes

dsDNA→ssRNA requires RNA polymerase (DNA dependent)

ssRNA→protein requires ribosomes

DNA replication requires DNA polymerase

bacteria and archaea have a lot of similarities, so can archaea also be in biofilms?

yes they can form their own biofilms and even be in mixed biofilms with bacteria

can archaea cause disease in humans like bacteria?

no, we are not aware of any archaea that can cause human and animal disease (mostly because they like the viral mechanisms to do so)

what is archaellum? what is it similar to?

it is an extracellular appendage that moves a cell through liquid. it is similar in structural appearance and motility to bacteria flagella

how are archaellum different from flagella? (3)

they differ in protein structure and the rotation mechanism AND

specifically, bacteria flagella are powered via proton gradients while archaea power archaellum via ATP (*note: the proton gradient in bacteria does power ATP synthesis but the ATP does not directly power the flagella like it does the archaellum in archaea)

are archaellum only used for motility?

no, they are hypothesized to also help with attachment to other archaea but are not hollow like cannulae (so no passing of material)

what is distinctive about the genus haloquadratum?

it is a genus unique to archaea and indicates the square “wafer thin” structure some archaea have with little cytoplasmic chape

what are two benefits for archaea to have the square morphology?

they have a maximized surface area to volume ratio

can efficiently back together in biofilms

how do archaea maintain their square shape?

with unique actin-like proteins (actin=protein found in eukarytoes that maintain cellular shape)

do all archaea have cell walls?

some do but not all (not as consistent compared to bacteria) (they do have the cytoplasmic membrane)

what is unique about the composition of archaea cell walls compared to bacterial cell walls? 2)

archaea DO NOT have traditional peptidoglycan but have pseudopeptidoglycan (which is similar to peptidogylcan).

they also do have traditional NAG but not NAM. instead of NAM they have NAT (aka N-acetyltalosaminuronic acid)

wat will happen if you do a gram stain on archaea?

you will get mixed results because archaea vary so much in their cell wall thickness

how are archaeal lipids different than eukaryotic and bacterial lipids? (2)

1. they use L-glycerol and not D-glycerol

2. have ether (R-O-R) and not ester (R-COO-R)

what are similarities between the archaeal genome and the bacterial genome (4)

• circular genome (one circular chromosome)

• have similar gene size and density

• both have operons (and regulons)

• both have polycistronic RNA (aka RNA that encodes for multiple proteins)

what are some differences between archaeal genome and bacterial genome?

archaea have…

• introns (spliced out)

• noncoding RNA (think of it as functional RNA like tRNA)

• histone homologs (proteins that organize and compact DNA→archaea mainly use this for stabilizing DNA rather than compacting=found in eukaryotes)

*reminder you can look at sequencing of DNA and RNA to distinguish the two

how is ammonia found on the skin and where? what is its effect? how does our body mitigate this effect?

ammonia (NH3) is a byproduct of protein metabolism, so it accumulates on the skin (especially in hair follicles or sebaceous glands where kertain and sebum are abundant)

its effect: it can disrupt skin pH balance, leading to irritation or dryness

how to mitigate: there are methanogens (archaea) that metabolize ammonia to convert into less harmful substances, like ammonium ions (NH4+) or methane

what does the human microbiome consist of? list in decreasing abundancy

non-disease causing:

bacteria (most)

fungi

archea (least)

viruses (still a little unclear because the components must not cause disease)

where is the human microbiome found? aka on what areas of the body can you find the human microbiome?

any area that has a route to the environment like the skin and digestive tract (these two are the most commonly known) + respiratory tract and urogenital/urinary tract

*you will not find the microbiome on the brain, bones, or pancreas (aka has no route to environment)

what happens if some flora in the microbiome change behavior or move?

it can go into a different area and cause infection

what is distinct about eukaryotes?

their structure is defined by a nucleus and membrane bound organelles (even if it is unicellular)

are all eukaryotes disease causing?

no but some can be

what does the cell wall of fungi consist of? what about its membrane?

cell wall: chitin (protective polysaccharide)

membrane: ergosterol

what do fungi absolutely need to live (1)

ergosterol for their membranes

what method do all fungi use to get their nutrients?

absorptive nutrition: they will secrete enzymes outside of the cell to break down complex substances into simpler nutrients

are all fungi multicellular?

no: they can be unicellular (yeast) or multicellular (mold)

what kind of environment do fungi prefer to live in?

damp, moist environments

little reminder: what does asexual and sexual reproduction result in?

asexual: identical daughter cells

sexual: gametes (half of genetic material)→will result in unique daughter cell once combined with another gamete

what are the individual components of mold? what do we call the entire interconnected network

individual component: hyphae

whole network: mycelium

morphology of mold

it is filamentous or branching shape (long thread-like hyphae forming mycelium)

morphology of yeast

teardrop of egg shape

reproduction mechanism of mold

asexual via spores and some sexual (gametes)

reproduction mechanism of yeast

asexual via budding or fission, some sexual reproduction

growth form of mold

they make visible colonies (fuzzy, cottony, and can be multi-color)

growth form of yeast

smooth, moist colonies (like bacteria) (cream color)

habitat of mold

damp, decaying organic matter, soil, or food

habitat of yeast

on fruit, plant surfaces, or mucous membranes

examples of mold

aspergillus, penicillium, and rhizopus

examples of yeast

Saccharomyces cerevisiae or Candida albicans