Unit II- Dynamic Genomes and the Creation of Genetic Diversity Flashcards
1
Q
Why is genetic variation/instability important
A
-fodder for natural selection (can be costly to the individual but beneficial to the population)
-leads to the propagation of drug resistant micro-organisms
-implications for human health
(-uncovering of recessive genetic diseases
-deregulation of normal genes (cancer)
-susceptibility/resistance to disease
-response to treatment)
2
Q
Why you need to understand genetic variation in bacteria
A
- models the same processes in our cells (recombination, new mutations, viruses, transposable elements)
- the mechanisms lead to induction and propagation of antibiotic resistance
- to introduce plasmids, a critical tool for recombinant DNA technology
3
Q
New mutations- genetic variation
A
- mistakes during DNA replication and DNA repair (greatest source of small lesions: 1/10^9 per nucleotide per replication in bacteria, 1/10^7 in yeast, 1/10^6 in humans
- chromosomal rearrangements caused by inappropriate recombination events and/or the insertion of mobile elements (greatest source of large lesions)
4
Q
Spontaneous mutations and natural selection in E. coli
A
- haploid
- genome is encoded on a dsDNA circular chromosome of 4-5,000,000 base pairs
- doubles every 20 minutes
- mutation rate is 1/10^9 per nucleotide per replication. In 10^9 per nucleotide per replication. IN 10^9 cells there are likely to be many mutations represented in the population
5
Q
Gene transfer in bacteria via mating
A
- F+ bacteria can mate with F- bacteria
- F+ bacteria can form a sex pilus
- small epigenetic elements such as plasmids can be transferred via the pilus
- F+ status is conferred by F plasmids
6
Q
Plasmids
A
- small circular, dsDNA molecules that are distinct from the bacterial chromosome
- carry sequence elements that allow for replication and other goodies (F Plasmids carry genes required to make the sex pilus and transfer DNA to the recipient by rolling circle replication)
- plasmids are used to manipulate, amplify and purify exogenous DNA sequences
- common way bacteria spread drug resistance
- 1/3 of Neisseria gonorhoeae isolates are pencillin resistant
7
Q
Bacterial Transformation
A
- some strains of bacteria (Bacillus subtilis) can pick up DNA from their environment
- DNA may come from the lysis of other bacteria
- the exogenous DNA can be incorporated into the bacteria chromosome (recombination)
8
Q
Homologous Recombination in Bacteria
A
- this is the reciprocal exchange of genetic information (DNA)
- two homologous sequences align so they are in register
- both strands of each double helix are broken and rejoined to the homologue
- exchange can occur anywhere in the region of homology
- fidelity is high; the sequence at the site of exchange usually remains unaltered
9
Q
gene transfer by bacteria viruses (bacteriophases)
A
-viruses are parasites that cannot replicate themselves without a host
- genomes express:
- coat proteins that serve to package, protect and help deliver the genome to a new host
- other activities required to replicate, express or integrate the virus genome into the host chromosome
- possibly genes picked up from previous hosts
-bacteriaphage lambda: dsDNA virus that has been used to manipulate exogenous DNA sequences in E. coli
10
Q
Mechanism of bacterial recombination
A
- the process initiates with the alignment in register of two homologues, double stranded DNA sequences
- a nick is made in one strand allowing it to invade and anneal to the complementary strand of the homologue (called strand exchange)
- then the displaced strand is nicked and it anneals to the other homologue at which point the ends are ligated to complete formation of cross-strand exchange (Holiday junction)
- the DNA strands have to get the outside strands to cross each other
- then the crossing strand are cut and ligated to each other
11
Q
Integration of DNA by recombination
A
- double crossovers by homologous recombination can lead to integration of an exogenous DNA fragment into the bacterial chromosome
- this would lead to a stable transformation event
- in addition plasmids can integrate into the bacterial chromosomes via short regions of homology
- both mechanisms are used to transfer antibiotic resistance genes
12
Q
Latent versus Lytic virus
A
- integration results in a latent stage referred to as the prophage
- integration occurs by site-specific recombination catalyzed by a virus encoded integrase
- in lysis the virus just makes the cell make the proteins needed to make new virus and after they are packaged the cell explodes
13
Q
Movement of genes by transduction
A
- when the bacteriophages are induced to exise themselves from the bacterial chromosome, they can pick up flanking DNA
- this flanking DNA will be packaged into viral particles that can infect new hosts
- transfer of bacterial genes in this manner is called transduction
14
Q
Transposons
A
- integrate into the bacterial chromosome, frequently in multiple copies
- range in length from several hundred to several thousands of base pairs
- 10-20 transposons per bacterium
- codes for at least a transposase that catalyzes transposition
- may also carry antibiotic resistance genes that can be transfered to other cells by hopping into plasmids or bacteriophages
- insertion can disrupt a gene
15
Q
Bacterial transposons
A
IS3, Tn3, and Tn10
- they can cut from the original site and insert into a new site: non-replicative transposition (cut-and-paste)
- or they can be copied by DNA replication and then insert into new site, amplification: replicative transposition
