| DNA does not perserve well, however | lipids are not as diverse and not very specific biomarkers - compared to lipids the taxonomic potential is very high for DNA |
| the RNA | uses the information in the genome, cell taking advantage of the capabilities stored in dna |
| ribosome | site of protein synthesis, made up of RNA and proteins |
| mRNA | makes (structural and enxymatic) proteinsfrom gene transcription |
| genome | total 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 ancestor | LUCA -> origin of all forms of life |
| Bacteria can acquire DNA from other organisms/outside through | horizontal 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 place | sulphate methane transition zone - CH4 + SO42- HCO3- + HS- + H2O |
| Ancient DNA can help in assigning biological sources, an example is | where 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 of | evolution 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 surrogate | Tetrahymanol (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 by | bacteria and eukaryotes mainly |
| ether bonds are mainly made by | archaea (though bacteria can too) |
| Uk 37 who and what | long chain alkenones, haptophyte algae |
| TEX86 who and what | isoprenoid GDGTs, thaumarchaeota |
| LDI who and what | long chain diols, eustigmatophytes |
| BIT who and what | branched GDGTs, bacteria (terrestrial) |
| Problems with TEX | changes 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 |
