Microbial Genetics (12) Flashcards
(21 cards)
Genomics
mapping, sequencing, analyzing, and comparing genomes.
what does genomics look at?
Entire complement of genetic information: genes, regulatory systems & non-coding regions
Genome Sequencing
- DNA fragmentation
- DNA cloned into Plasmids & insert sequenced. (shot gun sequencing, want 10X overlap)
- “read” with biology software
Open reading Frames
Can look for distinguishing things: promotor, shine dalgarno, start codon, stop codon, terminator.
- suggests you have a gene.
- bacteria - genes reading in both directions
What is the general pattern for size of an organism and lifestyle?
Endosymbioants = small genome, small # ORF
- Parasites in the middle
- Free living largest genomes, most ORF’s.
- viable cell - 250-300 genes min.
Bioinformatics
Compuational tools for nucleic acid and protein sequences.
- storage & access
- statistical analysis
- comparative analysis
Comparative Analysis
- predict function of some genes based on homology (similarity to sequences of known function).
- may predict biochemical pathways or transport systems.
What genes are most abundant in prokaryotes?
metabolic genes
Uncharacterized ORF’s
- hypothetical proteins
- no homology
- don’t know function
- likely nonessential but evolutionarily adaptive
- maybe regulatory or redundant proteins
- maybe new activites
Chromosomal Islands
- DNA of foreign origin
- “extra” property (like virulance, symbiosis, diodegradation)
- contains all genes needed to function
- have inverted repeats, different GC composition, vary in other strains.
Core vs. Pan genome
Core: shared by all strains of a species
Pan: “optional extras” not present in all
Transcriptomics
Entire complement of RNA under specific conditions.
Look at transcripts and how produced at different conditions.
Microarrays
Used in transcriptomics. mRNA goes on chip and will bind to probes specific to genes. Under different conditions, different mRNA produced, get different patterns.
What can microarrays be used for?
- global gene expression
- expression under different conditions (regulons)
- expression genes of unknown function
- comparison gene content
- species identification
- doesn’t have to be mRNA
Proteomics
Study of structure, function and regulation of all proteins in a genome.
2D Gel Electrophoresis
Used for proteins.
1st dimension - horizontal, separated by isoelectric point
2nd dimension - vertical, denatured, separated by size.
Proteins and gene sequence similarity
> 70% sequence similarity, almost certainly similar functions.
What are protein domains?
- Distinct functional modules (highly conserved regions, like DNA binding domains, ATP hydrolysis)
- allow prediction of function without complete sequence homology
Metabolomics
All metabolic intermediates and small molecules produced by an organism.
- monitor by Mass Spectrometry
Metagenomics
Total gene content of organisms present in an enviornment
- may include: deep sea sediments, fertile soils, global ocean survey etc.
GOS
Global Ocean survary, Craig Venter, found many many novel protein sequences and families.
