Genomic Tools
What does PCR amplify?
A specific DNA target sequence
Sanger sequencing uses what special nucleotide?
ddNTPs (dideoxynucleotides)
What does a transcriptome measure?
All RNA expressed by a cell under certain conditions
What gene is the “gold standard” for bacterial phylogeny?
16S rRNA gene
Which group contains lactic acid–producing fermenters like Lactobacillus?
Firmicutes
What is the purpose of restriction enzymes?
To cut DNA at specific recognition sites
Which generation first introduced massively parallel sequencing?
Second-generation
What is hybridized onto a microarray chip?
Labeled cDNA/mRNA
Why is 16S rRNA useful for phylogeny?
Conserved, present in all cells, enough variable regions
What structure allows Caulobacter to attach to surfaces?
Holdfast on a stalk
Why is agarose gel electrophoresis useful?
It separates DNA by size using an electric field
Which technology measures pH changes when nucleotides are added?
Ion Torrent
What does RNA-seq give that microarrays do not?
Quantitative sequencing of all expressed transcripts
What is genetic drift?
Random change in allele frequencies
Which bacteria are predatory and invade the periplasm of prey?
Bdellovibrio
What defines a functional ORF?
Start codon, stop codon, Shine–Dalgarno sequence, and coding potential
Which platform sequences individual DNA molecules using fluorescent tags released at incorporation?
Single Molecule Real-Time (SMRT) sequencing
What does proteomics analyze?
Structure, function, and expression of all proteins
What major evolutionary event increased global oxygen levels?
Cyanobacterial oxygenic photosynthesis
What trait allows haloarchaea to survive high salt?
Pumping high intracellular K+ to balance osmotic pressure
Why is assembly required after shotgun sequencing?
Because the genome is fragmented and must be reconstructed using overlapping reads
Why are nanopore sequences particularly valuable for systematics?
They provide ultra-long reads that resolve structural variation & repetitive regions
What is metabolomics?
Analysis of all metabolic intermediates & small molecules
What distinguishes a rooted vs unrooted phylogenetic tree?
Rooted shows direction of evolution; unrooted shows relationships only
What are chlorosomes, and which bacteria have them?
Bacteriochlorophyll-rich light-harvesting structures in Green Sulfur Bacteria