I is correct ii is correct
Ecology:
16ATP+8e+8H+N2–>2NH3+H2. Nitrogenase irreversibly inactivated by O2==Leghmoglobin(pink) binds to O2, keeping free O2 low to protect nitrogenase, root nodule is physical barrier, respiration high in nodules| Plant provides sugar(glu) and rhizo, and rhizo fixes N2. Glutamate = lots of N2 glutamine = low N2| Plant make flavonoid, induce nod-factor(lipooligosaccharide). Nod-signal produced by bac (intiates symbiosis). Root curl (shep.Crook)after contact to stop cell growth, and initiate everything.
Archaea:Originally extremophiles due to only being found there. Found everywhere.|sequecned with 16S rRNA, b/c universal, but some (methanogens) didnt match euk or bac., so fundamentally different group|Methanogensis=only occurs in archaea, important in carbon cycle(b/c terminal step, helps with recycling) , greenhouse gas Methanogens=produce methane at the end of metabolism. CD+H2 or Acetate or methyl = methane.|believed to be distant relative of eukaryota. Ribo:close in structure and number 70S,some ribo. Prot. Only found in arch. And euk., tRNA: arch, use TATA (TBP, A-T rich sequence) and TFB and euk. Use TATA and TFIIB to initiate transcript.(bac dont do this.) RNA Poly: same multi-subunit complex similar to RNA Pol II in euk., Asgard Archaea: Lokiarchaeota, contain genes only though to belong to euk. (actin, tublin, ubiquitin systems)|Not like bac: ether-linked lipids, isporenoid chains, monolayer (not bi-layer), have introns (like euk.), no peptoglycan in cell wall like bac, so resistant to lysozyme(no substrate to hydrolyze to break bonds) and beta-lactam antibitoics (No Penicillin-binding proteins to bind to weaken.)MAIN GROUPS: TACK (extremophiles), Euryarchaeota (methanogens,thermophiles.), Asgard (thermovents, lokiarchaeota, DPANN(small genomes, need symbiotic partner). | BIOTECH: good for DNA polymerase for PCR(withstand the heating cycles), good for industrial enzymes (biofuel, food proccessing, hightemp. Chem. Reactions.) | remian stable at high temp, salt, and extreme pH’s.
Genomics:
Sanger Seq. Generates many fragments of dif. Lengths determined by dideoxynucleotides(ddNTPs), which then determien the seq.
Sanger starts wtih primer, adds in DNA pol., dNTPs and ddNTPs, synthesis terminates when ddNTP is added. Produces DNA frag. Of dif. Lengths that reveal the base at each position.1st did bacteria phage.| what abt larger fragments? Whole Genome shotgun seq: extracting organisms’s entire dna, fragmenting it into tiny pieces, then uses machines to read them, and realign them correctly. Identifies SNP compared to original. Hierarchial shotgun sequencing: cloning large segments into bac. Artificial chromosomes, inserting them into bac.(e.Coli) that creates a “library”. Find order and overlapping regions “tiling path” for correct order, then fragmented again to be placed backtogether in shotgun method.|MicroArray:
-uses hybridizaition on known 2 DNA probes -req. Prior knowledge of gene sequence – limited to genes in array – used for SNP genotyping is cheaper – samle DNA from PCR, then pathogenic DNA is tagged w/ dyes and pathogenic specific dna is present and hybridizes and fluoresence is observed.
RNA-seq
-next generation seq of cDNA -no prior knowledge needed – detects all transcripts present in sample – higher sensitivity and broader range -TOTAL RNA (trna, mrna, etc.) | illumina: – more precise -SNP detection (choose for transcriptomic studies, deep sequencing) Nanopore: – faster – reads longer fragments – portable – cheaper (choose for real-time sequencing.
Microbiome:
Microbiota
Microorganisms present on a bodies site Microbiome:
Microorganisms, their genes, products, and local environment. Metagenome: DNA recovered from environment representing the entire community(shotgun, amplicon(16S, who), functional(how, what) | commensalism (host unharmed, but also not helped), mutualism (e.Coli produces Vita. K) | Pre-biotics: specialized plant fibers that feed beneficial bac. In my gut., non-digestible Pro-biotics: live microorganisms that add to the bacteria in the gut.|Microbiome helps w/ protection against pathogens, synthesis of vitamins, immune system development, fat storage, modulation of CNS.|Most microbes in colon. | despite difference in microbiome, the functionality stays the same and at equalibrium for survival | Study Techniques: 16S rDNA(taxonomic composition), metagenomics (tax. Comp and functional pot.), metatranscriptomics/metabolomics move closer to activity.|C.Diff. Rebyota: fecal matter(not own.) , single-dose and admistered rectally to prevent recurrance. Vowst: FDA-approved orlaly admistered, microbiota derived from healthy human stool(not yours.) | Respiratory: upper airways have more microbiome. Healhy lungs have low biomass | gnotobiotic animals: germ-free or harbor know community of microorganisms. Used as “clean slate” (establishing casualities, determinig bacterial function, immune system development, microbial interactions.