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Questions and Answers List

level questions: Level 1

QuestionAnswer
DNA does not perserve well, howeverlipids are not as diverse and not very specific biomarkers - compared to lipids the taxonomic potential is very high for DNA
the RNAuses the information in the genome, cell taking advantage of the capabilities stored in dna
ribosomesite of protein synthesis, made up of RNA and proteins
mRNAmakes (structural and enxymatic) proteinsfrom gene transcription
genometotal DNA
DNA...tells you what he cell is capable of, but not if it actually did
16S ribosomal RNA can be used as a phylogenetic marker gene, for who and why?bacteria and archaea - it is specific to each genus
18S ribosomal RNA can be used as a phylogenetic marker gene for ...eukaryotes
Last universal common ancestorLUCA -> origin of all forms of life
Bacteria can acquire DNA from other organisms/outside throughhorizontal gene transfer (however this does ot work for 16S)
what problem can horizontal gene transfer by bacteria cause for us?bacteria gains from antibiotic and becomes resistant -> antibiotic resistance, makes it very hard to get rid of -> can pass this trait to others
Metagenomics =Sequencing DNA from many organisms at a time and separating and organising them -> allows analyses of complete genome, know complete DNA
Thaumarchaeota are ammonia oxidizing archaea (no light, need oxygen to oxidize ammonia but can make it in oxygen depleted environments), what gene codes for this?MOA
during the perm there was a syntrophic relation ship between mathanotrophic archaea (ANME, anaerobic methanotroph) and sulphare reducing bacteria. What was this transition zone called where this occured and what reaction took placesulphate methane transition zone - CH4 + SO42-  HCO3- + HS- + H2O
Ancient DNA can help in assigning biological sources, an example iswhere we see a large change in biomarker signal, but dont undersand why -> DNA can show if there was a turnover or change in who made the biomarker (species) -> however, don't know if this is the only source
Two ways of determining what a gene is doin?gain function/alternative hosting of gene & gene knockout
Diatoms make highly branched isoprenoids (HBI alkenes), however two taxonomically unrelated groups make them, how could this be?convergent evolution
botryoccoccus braunni (ancient algae, directly contributed to oil and coal shale deposits) makes both squalene and botryococcene, what is special about this?At firs tonly squalene synthesis, but gene duplicated and modified to also start synthesis botryococcene (development of new pathway)
Hopanoids are lipid compounds commonly found in the membranes of bacteria. Squalene can be transformed into hopane through ....squalene hopane cyclase shc
2-methylhopanes are biosynthesised by cyanobacteria (oxygenic photosynthetic bacteria) and are found in 2.7Gya shales, they are indicators ofevolution of oxygenic photosynthesis (produces oxygen) well before the atmosphere became oxidizing. HOWEVER 2-MeBHPs have been found in an anoxygenic phototroph! 2-methylhopanes can’t be used for biomarkers of oxygenic photosynthesis
Do sterols only occur in eukaryotes?Some bacteria with ancestral sterol biosynthetic pathway, however: less modified. Specific steranes are still valid as biomarkers of presence of O2 (aerobic bacteria), but not of the presence of eukaryotes
arboranes are biomarker of flowering plants/angiosperms (terrestrial input), however are also found in perm/triassicm why?some bacteria have gene to synthesise isoarborinol (osC gene) - so not very valid biomarker for plants
Tetrahymanol is biosynthesised by Tetrahymena Pyriformis, which is...a ciliated protozoan which is able to thrive in anoxic environments.
In anoxic systems sterol synthesis is inhibited due to lack of O2 (stratified anoxia?), ..... works there as a sterol surrogateTetrahymanol (converted to Gammacerane during diagenesis, so should be an anoxia/ stratification biomarker)
The porblem with tetrahymanol is..that not only eukaryotes make them, but bacteria can also
ester bonds are made bybacteria and eukaryotes mainly
ether bonds are mainly made byarchaea (though bacteria can too)
Uk 37 who and whatlong chain alkenones, haptophyte algae
TEX86 who and whatisoprenoid GDGTs, thaumarchaeota
LDI who and whatlong chain diols, eustigmatophytes
BIT who and whatbranched GDGTs, bacteria (terrestrial)
Problems with TEXchanges in circulation, seasonal production, selective export to sediments, different thaumarchaeota populations have differnt GDGT compositions with temperature (e.g., shallow vs deep response), other archaea contributing to GDGT composition
ether bond of archaea is ... that ester bond of (bacteria and eukaryotes)stronger -> live in harsher environments