bacterial genes and genomes Flashcards
(17 cards)
what is a genome?
the complete set of genes within a cell or living organism
what is genome assembly?
the process of ‘assembling’ two or more overlapping sequenced
DNA fragments into one continuous piece
why is genome assembly necessary?
It is virtually impossible to sequence the entire genome in one single piece
why is it virtually impossible to sequence the entire genome in one single piece?
There are physical limitations that prevent scientists from working with/handling
intact whole chromosomes and for short-read platforms like Illumina only short (50-
300bp) fragments are sequenced
Basic facts about bacteria
- Bacteria are prokaryotic and therefore do not possess a nucleus
- Bacteria typically possess one chromosome
- Bacterial chromosomes are usually circular
- Bacteria frequently harbour extra-chromosomal elements called plasmids.
genome annotation
the process of identifying functional elements (e.g. genes) within the
genome
How are genes organised in bacterial genomes?
Genes in bacteria are often organised into operons of genes with a related function/purpose
How are genes in the genome identified?
in order to identify a gene within a genome, an appropriate “open reading frame” must be
determined.
An Open Reading Frame or ORF is defined as the DNA between start and stop codons in the
same reading frame
what is the core genome?
shared by all members of a species
what is a pan genome?
includes the core genome + genes unique to that organism
what is the metagenome?
the total genetic complement of all the cells present in a particular
environment
what are the three types of mutational phenotypes
- Neutral to fitness (no selective pressure)
- Positive to fitness (positive selective pressure)
- Negative to fitness (negative selective pressure)
what is genetic recombination?
the exchange of genetic material between different
segments of DNA (or different DNAs entirely)
what genes in a genome are essential?
an essential gene cannot be ‘deleted’
Transposon sequencing (Tn-seq)
A transposon is a mobile genetic element that can move locations in the genome. Also
known as a ’jumping gene’ discovered by Barbara McClintock (1983 Nobel Prize winner)
what does the Assembly of the Pre-Initiation Complex require?
General Transcription Factors that Recruit Pol II
what do Upstream activators bind to
