Lecture 10 Microbial Genomics Flashcards Preview

BIO 425: Microbiology > Lecture 10 Microbial Genomics > Flashcards

Flashcards in Lecture 10 Microbial Genomics Deck (27)
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How do we sequence a genome?

Shotgun approach
-fragmentation = cut genome into small pieces
-sequencing = sequence each DNA piece
-assembly = put the pieces together


What is fragmentation?

First step in sequencing a genome
-cut the genome into small pieces
-through physical shearing or enzymatic methods


What is sequencing?

Second step of genome sequencing
-determining the nucleotide composition of DNA

Sequencing Methods
1. First Generation sequencing
2. Second generation sequencing
3. Third generation sequencing


What is the Sanger Dideoxy method?

First generation sequencing method
-does PCR with dideoxynucleotides which are analogs

Can do manual
-4 rxns
-1 for each nucleotide
-separate w/ gel electrophoresis

Can do automated
-single rxn w/ fluorescent markers fr each nucleotide


What is next generation sequencing?

Second generation sequencing method
-massivle parallel=diff sequences run together

Much fast and cheaper that 1st gen

Still requires amplification of DNA samples


What are the limitations of first generation sequencing?

one sequence at a time

multiple not possible


What are the methods and platforms of second generation sequencing?

454 Platform
-Uses Emulsion PCR

Illumina Platform
-Uses Bridge PCR


What is single molecule sequencing?

Third generation sequencing method
-massively parallel
-Real time results, the fastest method
-Does NOT require amplification of DNA samples


What are the methods and platforms of third generation sequencing?

Nanopore Platform
-Nanopore technology

Pacific Biosciences Platform
-Uses SMRT technology


What is assembly?

Last step of genome sequencing
-reconstructing genomes by combining short, overlapping DNA sequences


What are the types of assembly?

Reference alignment
-comparison to known genome
-must be closely related to organism

De novo assembly
-novel genome construction
-no close relative required


What is bioniformatics?

analyzing and storing DNA/Protein sequences using powerful computational tools
-Doing comparative analysis on genome size, content and organization


What is the difference between a small and large genome?

Small genome
-140,000 to 1,000,000 bp
-endosymbionts and parasites

Large genome
-5,000,000 to 13,000,000 bp
-free living organisms


How does gene content differ?

Larger genomes = more genes
-little 'junk' DNA

Essential Genes for life
-DNA replication
-translation for protein synthesis


What is annotation?

predicting functional genes from DNA sequence data
-uses comparative analysis


What is genomics? Transcriptomics? Proteomics?

Genomics - all genetic information in the cell
-metagenomics all genetic information in the environment

Transcriptomics - expressed genetic information

Proteomics - translated genetic information


What is metagenomics?

pooled DNA from an environmental smaple
-includes genes from many different organisms


What is transcriptomics?

Study of total gene expression


What are microarrays?

Gene chips
-silica chips containing different genes
-tracks expression levels of individual genes


What are the applications of transcriptomics?

study of pathogenic bacteria

study of human cancer cells


What is proteomics?

study of total protein production

In vitro
-separate and ID proteins

In silico
-predict proteins from DNA


How do genomes change over time?

Gene duplication

Gene deletion

Horizontal gene transfer


How do we compare genes?

Homologous genes
-simlar gene sequences from a common ancestor

-similar genes in two different organisms

-similar genes in the same organism
-arise from gene duplication


What is gene duplication?

segment of DNA copied in the genome
-main mechanism of new gene evolution
-one copy remains unchanged and functional
-one copy mutates to a new function


What is gene deletion?

loss of a segment of DNA in the genome
-common in endosymbionts and parasites

Dependence on host results in 'useless' genes


What are the mechanisms of genome evolution?

Spontaneous mutations
-errors in DNA replication

Transposable Elements
-jumping genes
-transposons+insertion sequences


What are Core and Pan Genomes?

Core Genome
-essential genes
-in ALL strains of a species

Pan Genome
-non-essential genes
-in SOME strains of a species